Aeropyrum pernix K1 is an aerobe, heterotroph, hyperthermophilic prokaryote that forms irregular colonies and was isolated from marine solfataric vent.
Gram-negative motile coccus-shaped colony-forming aerobe heterotroph hyperthermophilic genome sequence 16S sequence| @ref 20215 |
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Last LPSN update
2026-02-09 11:18:40 |
| Domain Archaea |
| Phylum Thermoproteota |
| Class Thermoprotei |
| Order Acidilobales |
| Family Acidilobaceae |
| Genus Aeropyrum |
| Species Aeropyrum pernix |
| Full scientific name Aeropyrum pernix Sako et al. 1996 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 4521 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | Medium recipe at MediaDive  | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l Na2S2O3 x 5 H2O 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 66792 | ASM1112v1 assembly for Aeropyrum pernix K1 | complete | GCA_000011125   | 272557.25  | 2923402010  | 272557 | 96.94 |  |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins. | Badel C, Bell SD. | Nat Microbiol | 10.1038/s41564-023-01540-6 | 2024 | | |
| The evolution of archaeal flagellar filaments. | Kreutzberger MAB, Cvirkaite-Krupovic V, Liu Y, Baquero DP, Liu J, Sonani RR, Calladine CR, Wang F, Krupovic M, Egelman EH. | Proc Natl Acad Sci U S A | 10.1073/pnas.2304256120 | 2023 | | |
| Genetics | Cell cycle characteristics of crenarchaeota: unity among diversity. | Lundgren M, Malandrin L, Eriksson S, Huber H, Bernander R. | J Bacteriol | 10.1128/jb.00330-08 | 2008 | |
| Metabolism | The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity. | Hansen T, Reichstein B, Schmid R, Schonheit P. | J Bacteriol | 10.1128/jb.184.21.5955-5965.2002 | 2002 | |
| Enzymology | Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins. | Akanuma S, Yamaguchi M, Yamagishi A. | PLoS One | 10.1371/journal.pone.0258821 | 2021 | |
| Metabolism | Structural and functional insights into Aeropyrum pernix OppA, a member of a novel archaeal OppA subfamily. | Balestrieri M, Gogliettino M, Fiume I, Pocsfalvi G, Catara G, Rossi M, Palmieri G. | J Bacteriol | 10.1128/jb.00899-10 | 2011 | |
| Metabolism | Enzymatic degradation of PrPSc by a protease secreted from Aeropyrum pernix K1. | Snajder M, Vilfan T, Cernilec M, Rupreht R, Popovic M, Juntes P, Serbec VC, Ulrih NP. | PLoS One | 10.1371/journal.pone.0039548 | 2012 | |
| Stress | Inhibitory effect of Maillard reaction products on growth of the aerobic marine hyperthermophilic archaeon Aeropyrum pernix. | Kim KW, Lee SB. | Appl Environ Microbiol | 10.1128/aem.69.7.4325-4328.2003 | 2003 | |
| Metabolism | Outside the unusual cell wall of the hyperthermophilic archaeon Aeropyrum pernix K1. | Palmieri G, Cannio R, Fiume I, Rossi M, Pocsfalvi G. | Mol Cell Proteomics | 10.1074/mcp.m900012-mcp200 | 2009 | |
| Genetics | Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. | Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL. | Proc Natl Acad Sci U S A | 10.1073/pnas.0609279104 | 2007 | |
| Enzymology | Highly stable L-lysine 6-dehydrogenase from the thermophile Geobacillus stearothermophilus isolated from a Japanese hot spring: characterization, gene cloning and sequencing, and expression. | Heydari M, Ohshima T, Nunoura-Kominato N, Sakuraba H. | Appl Environ Microbiol | 10.1128/aem.70.2.937-942.2004 | 2004 | |
| Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life. | Saito M, Sato A, Nagata S, Tamaki S, Tomita M, Suzuki H, Kanai A. | Genome Biol Evol | 10.1093/gbe/evz195 | 2019 | | |
| Metabolism | Induced fit and the catalytic mechanism of isocitrate dehydrogenase. | Goncalves S, Miller SP, Carrondo MA, Dean AM, Matias PM. | Biochemistry | 10.1021/bi300483w | 2012 | |
| Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway. | Benrezkallah D. | J Mol Graph Model | 10.1016/j.jmgm.2023.108700 | 2024 | | |
| Lipids | Effects of producing high levels of hyperthermophile-specific C25,C25-archaeal membrane lipids in Escherichia coli. | Yoshida R, Motoyama K, Ito T, Hemmi H. | Biochem Biophys Res Commun | 10.1016/j.bbrc.2024.150349 | 2024 | |
| Genetics | X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix. | Yamauchi T, Kikuchi M, Iizuka Y, Tsunoda M. | Acta Crystallogr F Struct Biol Commun | 10.1107/s2053230x24009518 | 2024 | |
| Self-assembly of Aeropyrum pernix bacilliform virus 1 (APBV1) major capsid protein and its application as building blocks for nanomaterials. | Sumikama Y, Takashima A, Mochizuki T, Sakuraba H, Ohshima T, Sugihara S, Suye SI, Satomura T. | Extremophiles | 10.1007/s00792-022-01284-x | 2022 | | |
| Enzymology | Bioprocess development to produce a hyperthermostable S-methyl-5'-thioadenosine phosphorylase in Escherichia coli. | Schollmeyer J, Waldburger S, Njo K, Yehia H, Kurreck A, Neubauer P, Riedel SL. | Biotechnol Bioeng | 10.1002/bit.28526 | 2023 | |
| A mutation in the S6 segment of the KvAP channel changes the secondary structure and alters ion channel activity in a lipid bilayer membrane. | Malik C, Ghosh S. | Amino Acids | 10.1007/s00726-022-03188-8 | 2022 | | |
| Genetics | Archaeal DNA replication initiation: bridging LUCA's legacy and modern mechanisms. | Dulermo R. | Front Microbiol | 10.3389/fmicb.2025.1561973 | 2025 | |
| Biochemical characterization and mutational analysis of a mismatch glycosylase from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5. | Wang L, Lin T, Oger P, Gong Y, Zhang L. | DNA Repair (Amst) | 10.1016/j.dnarep.2022.103321 | 2022 | | |
| Identification of novel components of the Ced and Ups systems in Saccharolobus islandicus REY15A. | Wu P, Zhang M, Kou Y, Liang S, Ni J, Huang Q, Shen Y. | mLife | 10.1002/mlf2.12163 | 2025 | | |
| Enzymology | Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP. | Shibanuma Y, Nemoto N, Yamamoto N, Sampei GI, Kawai G. | J Biochem | 10.1093/jb/mvaa043 | 2020 | |
| Total Synthesis and Structure Confirmation of trans-Anhydromevalonate-5-phosphate, a Key Biosynthetic Intermediate of the Archaeal Mevalonate Pathway. | Yasuno Y, Nakayama A, Saito K, Kitsuwa K, Okamura H, Komeyama M, Hemmi H, Shinada T. | J Nat Prod | 10.1021/acs.jnatprod.1c00615 | 2021 | | |
| Enhanced isoprenoid production in Escherichia coli cells harboring the archaeal mevalonate pathway. | Takahashi T, Saito T, Dohgami I, Ito T, Hemmi H. | Biochem Biophys Rep | 10.1016/j.bbrep.2025.102307 | 2025 | | |
| Modulation of Kv Channel Gating by Light-Controlled Membrane Thickness. | Yadav R, Pfeffermann J, Goessweiner-Mohr N, Glasnov T, Akimov SA, Pohl P. | Biomolecules | 10.3390/biom15050744 | 2025 | | |
| Periplasmic production of pernisine in Escherichia coli and determinants for its high thermostability. | Bahun M, Hartman K, Poklar Ulrih N. | Appl Microbiol Biotechnol | 10.1007/s00253-020-10791-w | 2020 | | |
| A [4Fe-4S] cluster resides at the active center of phosphomevalonate dehydratase, a key enzyme in the archaeal modified mevalonate pathway. | Komeyama M, Kanno K, Mino H, Yasuno Y, Shinada T, Ito T, Hemmi H. | Front Microbiol | 10.3389/fmicb.2023.1150353 | 2023 | | |
| Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification. | Himiyama T, Tsuchiya Y, Yonezawa Y, Nakamura T. | Bioconjug Chem | 10.1021/acs.bioconjchem.0c00587 | 2021 | | |
| Mining unique cysteine synthetases and computational study on thoroughly eliminating feedback inhibition through tunnel engineering. | Xu S, Li ZL, Li ZM, Liu HL. | Protein Sci | 10.1002/pro.5160 | 2024 | | |
| Enzymology | Thermostable Enzyme Variants in the Lower Mevalonate Pathway Improve Isoprenoid Production by Cell-Free Biocatalysis. | Sarnik SA, Martinsen MR, Korman TP, Schwartz DK, Kaar JL, Bomble YJ. | ACS Sustain Chem Eng | 10.1021/acssuschemeng.5c03763 | 2025 | |
| Ligand binding Pro-miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase. | Kiss-Szeman AJ, Takacs L, Jakli I, Banoczi Z, Hosogi N, Traore DAK, Harmat V, Perczel A, Menyhard DK. | Protein Sci | 10.1002/pro.70320 | 2025 | | |
| Metabolism | A L-proline/O2 biofuel cell using L-proline dehydrogenase (LPDH) from Aeropyrum pernix. | Tonooka A, Komatsu T, Tanaka S, Sakamoto H, Satomura T, Suye SI. | Mol Biol Rep | 10.1007/s11033-018-4328-z | 2018 | |
| Enhanced Site-Specific Fluorescent Labeling of Membrane Proteins Using Native Nanodiscs. | Ezsias B, Wolkenstein F, Goessweiner-Mohr N, Yadav R, Siligan C, Posch S, Horner A, Vargas C, Keller S, Pohl P. | Biomolecules | 10.3390/biom15020254 | 2025 | | |
| Antioxidative Activity of Methanolic and Water Extracts from the Hyperthermophilic Archaeon Aeropyrum pernix K1. | Skrt M, Jamnik P, Poklar Ulrih N. | Acta Chim Slov | 10.17344/acsi.2017.3765 | 2018 | | |
| Stereospecific Enzymatic Conversion of Boronic Acids to Amines. | Hanley D, Li ZQ, Gao S, Virgil SC, Arnold FH, Alfonzo E. | J Am Chem Soc | 10.1021/jacs.4c04190 | 2024 | | |
| MicroED Structure of a Protoglobin Reactive Carbene Intermediate. | Danelius E, Porter NJ, Unge J, Arnold FH, Gonen T. | J Am Chem Soc | 10.1021/jacs.2c12004 | 2023 | | |
| Enzymology | Identification of six important amino acid residues of MenA from Bacillus subtilis natto for enzyme activity and formation of menaquinone. | Hu LX, Feng JJ, Wu J, Li W, Gningue SM, Yang ZM, Wang Z, Liu Y, Xue ZL. | Enzyme Microb Technol | 10.1016/j.enzmictec.2020.109583 | 2020 | |
| Biocatalytic Carbene Transfer Using Diazirines. | Porter NJ, Danelius E, Gonen T, Arnold FH. | J Am Chem Soc | 10.1021/jacs.2c02723 | 2022 | | |
| Metabolism | Biosynthetic machinery for C25,C25-diether archaeal lipids from the hyperthermophilic archaeon Aeropyrum pernix. | Yoshida R, Yoshimura T, Hemmi H. | Biochem Biophys Res Commun | 10.1016/j.bbrc.2018.02.028 | 2018 | |
| Metabolism | NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA. | Deng YJ, Feng L, Zhou H, Xiao X, Wang FP, Liu XP. | DNA Repair (Amst) | 10.1016/j.dnarep.2018.03.005 | 2018 | |
| Genetics | Archaeal Orc1 protein interacts with T-rich single-stranded DNA. | Wegrzyn K, Konieczny I. | BMC Res Notes | 10.1186/s13104-021-05690-w | 2021 | |
| Recombinant Expression of Archaeal Superoxide Dismutases in Plant Cell Cultures: A Sustainable Solution with Potential Application in the Food Industry. | Gogliettino M, Arciello S, Cillo F, Carluccio AV, Palmieri G, Apone F, Ambrosio RL, Anastasio A, Gratino L, Carola A, Cocca E. | Antioxidants (Basel) | 10.3390/antiox11091731 | 2022 | | |
| An enzyme-centric approach for constructing an amperometric l-malate biosensor with a long and programmable linear range. | Matthews CJ, Patrick WM. | Protein Sci | 10.1002/pro.4743 | 2023 | | |
| Production of the Sesquiterpene Bisabolene From One- and Two-Carbon Compounds in Engineered Methanosarcina acetivorans. | Mentrup A, Scheitz LV, Wallenfang T, Rother M. | Microb Biotechnol | 10.1111/1751-7915.70105 | 2025 | | |
| Enzymology | Enzymological characteristics of a novel archaeal dye-linked D-lactate dehydrogenase showing loose binding of FAD. | Satomura T, Hayashi J, Ohshida T, Sakuraba H, Ohshima T, Suye SI. | Extremophiles | 10.1007/s00792-018-1054-3 | 2018 | |
| The role of tRNA identity elements in aminoacyl-tRNA editing. | Cruz E, Vargas-Rodriguez O. | Front Microbiol | 10.3389/fmicb.2024.1437528 | 2024 | | |
| RNA Aptamers for a tRNA-Binding Protein from Aeropyrum pernix with Homologous Counterparts Distributed Throughout Evolution. | Ohmori S, Wani M, Kitabatake S, Nakatsugawa Y, Ando T, Umehara T, Tamura K. | Life (Basel) | 10.3390/life10020011 | 2020 | | |
| Phylogeny | Evolution of sequence, structural and functional diversity of the ubiquitous DNA/RNA-binding Alba domain. | Jagadeesh J, Vembar SS. | Sci Rep | 10.1038/s41598-024-79937-4 | 2024 | |
| Alteration of molecular assembly of peroxiredoxins from hyperthermophilic archaea. | Nakamura T, Oshima M, Yasuda M, Shimamura A, Morita J, Uegaki K. | J Biochem | 10.1093/jb/mvx045 | 2017 | | |
| Genome mining of cryptic bisabolenes that were biosynthesized by intramembrane terpene synthases from Antrodia cinnamomea. | Hewage RT, Tseng CC, Liang SY, Lai CY, Lin HC. | Philos Trans R Soc Lond B Biol Sci | 10.1098/rstb.2022.0033 | 2023 | | |
| Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery. | Beltran LC, Cvirkaite-Krupovic V, Miller J, Wang F, Kreutzberger MAB, Patkowski JB, Costa TRD, Schouten S, Levental I, Conticello VP, Egelman EH, Krupovic M. | Nat Commun | 10.1038/s41467-023-36349-8 | 2023 | | |
| Metabolism | Preparation of 1L-myo-Inositol 1-Phosphate as a Substrate of Phosphatidylinositol Phosphate Synthase. | Morii H, Nishimura T, Takeo M, Katayama C, Nakai K. | J UOEH | 10.7888/juoeh.40.217 | 2018 | |
| Kalium 3.0 is a comprehensive depository of natural, artificial, and labeled polypeptides acting on potassium channels. | Krylov NA, Tabakmakher VM, Yureva DA, Vassilevski AA, Kuzmenkov AI. | Protein Sci | 10.1002/pro.4776 | 2023 | | |
| Enzymology | The Radical SAM Heme Synthase AhbD from Methanosarcina barkeri Contains Two Auxiliary [4Fe-4S] Clusters. | Fix I, Heidinger L, Friedrich T, Layer G. | Biomolecules | 10.3390/biom13081268 | 2023 | |
| New components of the community-based DNA-repair mechanism in Sulfolobales. | Recalde A, Wagner A, Sivabalasarma S, Yurmashava A, Fehr NP, Thurm R, Le TN, Koebler C, Wassmer B, Albers SV, van Wolferen M. | Microlife | 10.1093/femsml/uqaf002 | 2025 | | |
| Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix. | Murakami R, Miyoshi T, Uchiumi T, Ito K. | Proteins | 10.1002/prot.25009 | 2016 | | |
| Metabolism | Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes. | Liebensteiner MG, Pinkse MW, Nijsse B, Verhaert PD, Tsesmetzis N, Stams AJ, Lomans BP. | Environ Microbiol Rep | 10.1111/1758-2229.12335 | 2015 | |
| Using several pseudo amino acid composition types and different machine learning algorithms to classify and predict archaeal phospholipases. | Samman N, Mohabatkar H, Rabiei P. | Mol Biol Res Commun | 10.22099/mbrc.2023.47756.1845 | 2023 | | |
| A thermophilic 8-oxoguanine DNA glycosylase from Thermococcus barophilus Ch5 is a new member of AGOG DNA glycosylase family | Wang L, Jiang D, Zhang L. | Acta Biochim Biophys Sin (Shanghai) | 10.3724/abbs.2022072 | 2022 | | |
| Heme A synthase in bacteria depends on one pair of cysteinyls for activity. | Lewin A, Hederstedt L. | Biochim Biophys Acta | 10.1016/j.bbabio.2015.11.008 | 2016 | | |
| Enzymology | Enantioselective Resolution of gamma-Lactam by a Novel Thermostable Type II (+)-gamma-Lactamase from the Hyperthermophilic Archaeon Aeropyrum pernix. | Ren L, Zhu S, Shi Y, Gao S, Zheng G. | Appl Biochem Biotechnol | 10.1007/s12010-015-1565-7 | 2015 | |
| Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis. | Gao S, Wu F, Gurcha SS, Batt SM, Besra GS, Rao Z, Zhang L. | Nat Microbiol | 10.1038/s41564-024-01643-8 | 2024 | | |
| Genetics | Archaea Microbiome Dysregulated Genes and Pathways as Molecular Targets for Lung Adenocarcinoma and Squamous Cell Carcinoma. | Uzelac M, Li Y, Chakladar J, Li WT, Ongkeko WM. | Int J Mol Sci | 10.3390/ijms231911566 | 2022 | |
| Lipids | Bilayer-Forming Lipids Enhance Archaeal Monolayer Membrane Stability. | Saracco M, Schaeffer P, Tourte M, Albers SV, Louis Y, Peters J, Deme B, Fontanay S, Oger PM. | Int J Mol Sci | 10.3390/ijms26073045 | 2025 | |
| Phylogeny | Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms. | Boya BR, Kumar P, Lee JH, Lee J. | Microorganisms | 10.3390/microorganisms9102156 | 2021 | |
| Enzymology | Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. | Menyhard DK, Orgovan Z, Szeltner Z, Szamosi I, Harmat V. | Acta Crystallogr D Biol Crystallogr | 10.1107/s1399004714026819 | 2015 | |
| Metabolism | Structure of the Prx6-subfamily 1-Cys peroxiredoxin from Sulfolobus islandicus. | Stroobants S, Van Molle I, Saidi Q, Jonckheere K, Maes D, Peeters E. | Acta Crystallogr F Struct Biol Commun | 10.1107/s2053230x19006472 | 2019 | |
| Metabolism | TK2268 encodes the major aminotransferase involved in the conversion from oxaloacetic acid to aspartic acid in Thermococcus kodakarensis. | Su Y, Michimori Y, Fukuyama Y, Shimamura S, Nunoura T, Atomi H. | Appl Environ Microbiol | 10.1128/aem.02017-24 | 2025 | |
| Reactivity of a Recombinant Esterase from Thermus thermophilus HB27 in Aqueous and Organic Media. | Gonzalez-Gonzalez R, Fucinos P, Beneventi E, Lopez-Lopez O, Pampin B, Rodriguez R, Gonzalez-Siso MI, Cruces J, Rua ML. | Microorganisms | 10.3390/microorganisms10050915 | 2022 | | |
| Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension. | Morris RG, Turner MS. | Phys Rev Lett | 10.1103/physrevlett.115.198101 | 2015 | | |
| Metabolism | Structure features of Streptococcus pneumoniae FabG and virtual screening of allosteric inhibitors. | Xu K, Zhong J, Li J, Cao Y, Wei L. | Front Mol Biosci | 10.3389/fmolb.2024.1472252 | 2024 | |
| Archaeal mevalonate pathway in the uncultured bacterium Candidatus Promineifilum breve belonging to the phylum Chloroflexota. | Kanno K, Kuriki R, Yasuno Y, Shinada T, Ito T, Hemmi H. | Appl Environ Microbiol | 10.1128/aem.01106-24 | 2024 | | |
| Enzymology | Identification and characterization of a novel (+)-gamma-lactamase from Microbacterium hydrocarbonoxydans. | Gao S, Huang R, Zhu S, Li H, Zheng G. | Appl Microbiol Biotechnol | 10.1007/s00253-016-7643-0 | 2016 | |
| Metabolism | Substrate specificity of undecaprenyl diphosphate synthase from the hyperthermophilic archaeon Aeropyrum pernix. | Mori T, Ogawa T, Yoshimura T, Hemmi H. | Biochem Biophys Res Commun | 10.1016/j.bbrc.2013.05.081 | 2013 | |
| Pathogenicity | Cytotoxicity and uptake of archaeosomes prepared from Aeropyrum pernix lipids. | Napotnik TB, Valant J, Gmajner D, Passamonti S, Miklavcic D, Ulrih NP. | Hum Exp Toxicol | 10.1177/0960327113477875 | 2013 | |
| Insights into the Maturation of Pernisine, a Subtilisin-Like Protease from the Hyperthermophilic Archaeon Aeropyrum pernix. | Bahun M, Snajder M, Turk D, Poklar Ulrih N. | Appl Environ Microbiol | 10.1128/aem.00971-20 | 2020 | | |
| Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation. | Yang X, Wang J, Li S, Li X, Gong J, Yan Z, Zhou H, Wu C, Liu X. | Nucleic Acids Res | 10.1093/nar/gkad525 | 2023 | | |
| Proteome | Deep learning reveals antibiotics in the archaeal proteome. | Torres MDT, Wan F, de la Fuente-Nunez C. | Nat Microbiol | 10.1038/s41564-025-02061-0 | 2025 | |
| Phylogeny | Malivhu: A Comprehensive Bioinformatics Resource for Filtering SARS and MERS Virus Proteins by Their Classification, Family and Species, and Prediction of Their Interactions Against Human Proteins. | Guevara-Barrientos D, Kaundal R. | Bioinform Biol Insights | 10.1177/11779322241263671 | 2024 | |
| A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides. | Charoenkwan P, Chotpatiwetchkul W, Lee VS, Nantasenamat C, Shoombuatong W. | Sci Rep | 10.1038/s41598-021-03293-w | 2021 | | |
| Thermoacidophilic Alicyclobacillus Superoxide Dismutase: Good Candidate as Additives in Food and Medicine. | Dong X, Wang W, Li S, Han H, Lv P, Yang C. | Front Microbiol | 10.3389/fmicb.2021.577001 | 2021 | | |
| Enzymology | Highly Efficient Multi-Step Oxidation Bioanode Using Microfluidic Channels. | Komatsu T, Hishii K, Kimura M, Amaya S, Sakamoto H, Takamura E, Satomura T, Suye SI. | Int J Mol Sci | 10.3390/ijms222413503 | 2021 | |
| Metabolism | Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans-anhydromevalonate 5-phosphate. | Hayakawa H, Motoyama K, Sobue F, Ito T, Kawaide H, Yoshimura T, Hemmi H. | Proc Natl Acad Sci U S A | 10.1073/pnas.1809154115 | 2018 | |
| Enzymology | Two-step efficient synthesis of 5-methyluridine via two thermostable nucleoside phosphorylase from Aeropyrum pernix. | Zhu S, Ren L, Wang J, Zheng G, Tang P. | Bioorg Med Chem Lett | 10.1016/j.bmcl.2011.12.142 | 2012 | |
| Enzymology | Studies on crenarchaeal tyrosylation accuracy with mutational analyses of tyrosyl-tRNA synthetase and tyrosine tRNA from Aeropyrum pernix. | Iwaki J, Endo K, Ichikawa T, Suzuki R, Fujimoto Z, Momma M, Kuno A, Nishimura S, Hasegawa T. | J Biochem | 10.1093/jb/mvs114 | 2012 | |
| Genetics | Two Family B DNA Polymerases From Aeropyrum pernix, Based on Revised Translational Frames. | Daimon K, Ishino S, Imai N, Nagumo S, Yamagami T, Matsukawa H, Ishino Y. | Front Mol Biosci | 10.3389/fmolb.2018.00037 | 2018 | |
| Metabolism | Biochemical characterization of RNase HII from Aeropyrum pernix. | Hou J, Liu Y, Lu Z, Liu X, Liu J. | Acta Biochim Biophys Sin (Shanghai) | 10.1093/abbs/gms011 | 2012 | |
| Donor strand complementation and calcium ion coordination drive the chaperone-free polymerization of archaeal cannulae. | Sleutel M, Sonani RR, Miller JG, Wang F, Gonzalez Socorro A, Chen Y, Martin R, Demeler B, Rudolph MJ, Alva V, Remaut H, Egelman EH, Conticello VP. | Nat Commun | 10.1038/s41467-025-64120-8 | 2025 | | |
| Enzymology | Gene expression and characterization of a third type of dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix. | Satomura T, Hara Y, Suye S, Sakuraba H, Ohshima T. | Biosci Biotechnol Biochem | 10.1271/bbb.110775 | 2012 | |
| Genome-Wide Identification of Superoxide Dismutase and Expression in Response to Fruit Development and Biological Stress in Akebia trifoliata: A Bioinformatics Study. | Yang H, Zhang Q, Zhong S, Yang H, Ren T, Chen C, Tan F, Cao G, Liu J, Luo P. | Antioxidants (Basel) | 10.3390/antiox12030726 | 2023 | | |
| Metabolism | Enhanced activity and enantioselectivity of a hyperthermophilic esterase from archaeon Aeropyrum pernix K1 by acetone treatment. | Cong F, Xing K, Gao R, Cao S, Zhang G. | Appl Biochem Biotechnol | 10.1007/s12010-011-9297-9 | 2011 | |
| Characterization of 2-phenanthroate:CoA ligase from the sulfate-reducing, phenanthrene-degrading enrichment culture TRIP. | Kaplieva-Dudek I, Samak NA, Bormann J, Kaschani F, Kaiser M, Meckenstock RU. | Appl Environ Microbiol | 10.1128/aem.01296-24 | 2024 | | |
| Enzymology | Extracellular production of the engineered thermostable protease pernisine from Aeropyrum pernix K1 in Streptomyces rimosus. | Snajder M, Carrillo Rincon AF, Magdevska V, Bahun M, Kranjc L, Pas M, Juntes P, Petkovic H, Poklar Ulrih N. | Microb Cell Fact | 10.1186/s12934-019-1245-3 | 2019 | |
| Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study. | Polak A, Tarek M, Tomsic M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavcic D. | Langmuir | 10.1021/la5014208 | 2014 | | |
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| Metabolism | The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange. | Fenyk S, Dixon CH, Gittens WH, Townsend PD, Sharples GJ, Palsson LO, Takken FL, Cann MJ. | J Biol Chem | 10.1074/jbc.m115.698589 | 2016 | |
| Structural basis for translation termination by archaeal RF1 and GTP-bound EF1alpha complex. | Kobayashi K, Saito K, Ishitani R, Ito K, Nureki O. | Nucleic Acids Res | 10.1093/nar/gks660 | 2012 | | |
| Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding. | Hung CH, Hwang TS, Chang YY, Luo HR, Wu SP, Hsu CH. | PLoS One | 10.1371/journal.pone.0083091 | 2013 | | |
| Exclusive use of trans-editing domains prevents proline mistranslation. | Vargas-Rodriguez O, Musier-Forsyth K. | J Biol Chem | 10.1074/jbc.m113.467795 | 2013 | | |
| Metabolism | Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX. | Kobayashi K, Masuda T, Tajima N, Wada H, Sato N. | Genome Biol Evol | 10.1093/gbe/evu170 | 2014 | |
| Metabolism | A green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms. | Hammon J, Palanivelu DV, Chen J, Patel C, Minor DL. | Protein Sci | 10.1002/pro.18 | 2009 | |
| Metabolism | Portability of paddle motif function and pharmacology in voltage sensors. | Alabi AA, Bahamonde MI, Jung HJ, Kim JI, Swartz KJ. | Nature | 10.1038/nature06266 | 2007 | |
| Enzymology | The phosphoenolpyruvate carboxylase from Methanothermobacter thermautotrophicus has a novel structure. | Patel HM, Kraszewski JL, Mukhopadhyay B. | J Bacteriol | 10.1128/jb.186.15.5129-5137.2004 | 2004 | |
| Metabolism | Functional analysis of the validamycin biosynthetic gene cluster and engineered production of validoxylamine A. | Bai L, Li L, Xu H, Minagawa K, Yu Y, Zhang Y, Zhou X, Floss HG, Mahmud T, Deng Z. | Chem Biol | 10.1016/j.chembiol.2006.02.002 | 2006 | |
| Stress | Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. | Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings Rd, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M. | PLoS One | 10.1371/journal.pone.0009773 | 2010 | |
| SORGOdb: Superoxide Reductase Gene Ontology curated DataBase. | Lucchetti-Miganeh C, Goudenege D, Thybert D, Salbert G, Barloy-Hubler F. | BMC Microbiol | 10.1186/1471-2180-11-105 | 2011 | | |
| Rigorous performance evaluation in protein structure modelling and implications for computational biology. | Moult J. | Philos Trans R Soc Lond B Biol Sci | 10.1098/rstb.2005.1810 | 2006 | | |
| Enzymology | Unique presence of a manganese catalase in a hyperthermophilic archaeon, Pyrobaculum calidifontis VA1. | Amo T, Atomi H, Imanaka T. | J Bacteriol | 10.1128/jb.184.12.3305-3312.2002 | 2002 | |
| Metabolism | CysK2 from Mycobacterium tuberculosis is an O-phospho-L-serine-dependent S-sulfocysteine synthase. | Steiner EM, Both D, Lossl P, Vilaplana F, Schnell R, Schneider G. | J Bacteriol | 10.1128/jb.01851-14 | 2014 | |
| Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. | Boekhorst J, Snel B. | BMC Bioinformatics | 10.1186/1471-2105-8-356 | 2007 | | |
| Genetics | Evolutionary analysis by whole-genome comparisons. | Bansal AK, Meyer TE. | J Bacteriol | 10.1128/jb.184.8.2260-2272.2002 | 2002 | |
| Metabolism | Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal "Shock" Reveal Generic and Specific Metal Responses. | Wheaton GH, Mukherjee A, Kelly RM. | Appl Environ Microbiol | 10.1128/aem.01176-16 | 2016 | |
| Metabolism | Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme. | Ahmad S, Muthukumar S, Kuncha SK, Routh SB, Yerabham AS, Hussain T, Kamarthapu V, Kruparani SP, Sankaranarayanan R. | Nat Commun | 10.1038/ncomms8552 | 2015 | |
| Metabolism | Sulfolobus replication factor C stimulates the activity of DNA polymerase B1. | Xing X, Zhang L, Guo L, She Q, Huang L. | J Bacteriol | 10.1128/jb.01552-14 | 2014 | |
| Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein. | Ghalei H, von Moeller H, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC. | Nucleic Acids Res | 10.1093/nar/gku259 | 2014 | | |
| Genetics | Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. | Koonin EV, Wolf YI, Aravind L. | Genome Res | 10.1101/gr.162001 | 2001 | |
| Metabolism | A tale of two oxidation states: bacterial colonization of arsenic-rich environments. | Muller D, Medigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsene-Ploetze F, Carapito C, Chandler M, Cournoyer B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lievremont D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Van Dorsselaer A, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN. | PLoS Genet | 10.1371/journal.pgen.0030053 | 2007 | |
| Phylogeny | Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. | Desmond E, Brochier-Armanet C, Gribaldo S. | BMC Evol Biol | 10.1186/1471-2148-7-106 | 2007 | |
| Insight into the proteome of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis: the major cytosolic and membrane proteins. | Burghardt T, Saller M, Gurster S, Muller D, Meyer C, Jahn U, Hochmuth E, Deutzmann R, Siedler F, Babinger P, Wirth R, Huber H, Rachel R. | Arch Microbiol | 10.1007/s00203-008-0399-x | 2008 | | |
| Metabolism | Structure and hydration of membranes embedded with voltage-sensing domains. | Krepkiy D, Mihailescu M, Freites JA, Schow EV, Worcester DL, Gawrisch K, Tobias DJ, White SH, Swartz KJ. | Nature | 10.1038/nature08542 | 2009 | |
| Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding. | Trasvina-Arenas CH, Cardona-Felix CS, Azuara-Liceaga E, Diaz-Quezada C, Brieba LG. | FEBS Open Bio | 10.1002/2211-5463.12209 | 2017 | | |
| Metabolism | Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. | Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP. | Proc Natl Acad Sci U S A | 10.1073/pnas.0502350102 | 2005 | |
| Metabolism | Microbial K+ channels. | Loukin SH, Kuo MM, Zhou XL, Haynes WJ, Kung C, Saimi Y. | J Gen Physiol | 10.1085/jgp.200509261 | 2005 | |
| Metabolism | Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis. | Poyraz O, Brunner K, Lohkamp B, Axelsson H, Hammarstrom LG, Schnell R, Schneider G. | PLoS One | 10.1371/journal.pone.0121494 | 2015 | |
| Metabolism | Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis. | Makarova KS, Koonin EV. | Archaea | 10.1155/2010/710303 | 2010 | |
| Enzymology | First characterization of an archaeal GTP-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. | Fukuda W, Fukui T, Atomi H, Imanaka T. | J Bacteriol | 10.1128/jb.186.14.4620-4627.2004 | 2004 | |
| The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life. | Atkinson GC. | BMC Genomics | 10.1186/s12864-015-1289-7 | 2015 | | |
| Metabolism | A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library. | Bartasun P, Cieslinski H, Bujacz A, Wierzbicka-Wos A, Kur J. | PLoS One | 10.1371/journal.pone.0055697 | 2013 | |
| Reconstitution of a transmembrane protein, the voltage-gated ion channel, KvAP, into giant unilamellar vesicles for microscopy and patch clamp studies. | Garten M, Aimon S, Bassereau P, Toombes GE. | J Vis Exp | 10.3791/52281 | 2015 | | |
| Metabolism | The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins. | Gray MJ, Tavares NK, Escalante-Semerena JC. | Mol Microbiol | 10.1111/j.1365-2958.2008.06437.x | 2008 | |
| Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target. | Spyrakis F, Singh R, Cozzini P, Campanini B, Salsi E, Felici P, Raboni S, Benedetti P, Cruciani G, Kellogg GE, Cook PF, Mozzarelli A. | PLoS One | 10.1371/journal.pone.0077558 | 2013 | | |
| Enzymology | Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance. | Miyazaki J, Asada K, Fushinobu S, Kuzuyama T, Nishiyama M. | J Bacteriol | 10.1128/jb.187.19.6779-6788.2005 | 2005 | |
| Enzymology | Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery. | Muller S, Urban A, Hecker A, Leclerc F, Branlant C, Motorin Y. | Nucleic Acids Res | 10.1093/nar/gkn1037 | 2009 | |
| Metabolism | A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides. | Nemoto TK, Ohara-Nemoto Y, Bezerra GA, Shimoyama Y, Kimura S. | J Biol Chem | 10.1074/jbc.m115.687566 | 2016 | |
| Enzymology | Cloning and characterization of archaeal type I signal peptidase from Methanococcus voltae. | Ng SY, Jarrell KF. | J Bacteriol | 10.1128/jb.185.20.5936-5942.2003 | 2003 | |
| Metabolism | Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features. | Bernick DL, Dennis PP, Hochsmann M, Lowe TM. | RNA | 10.1261/rna.031385.111 | 2012 | |
| Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair. | Yang H, Zhang T, Tao Y, Wang F, Tong L, Ding J. | Nucleic Acids Res | 10.1093/nar/gkt788 | 2013 | | |
| Structural and functional insights into the DNA replication factor Cdc45 reveal an evolutionary relationship to the DHH family of phosphoesterases. | Krastanova I, Sannino V, Amenitsch H, Gileadi O, Pisani FM, Onesti S. | J Biol Chem | 10.1074/jbc.m111.285395 | 2012 | | |
| Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. | Brochier-Armanet C, Forterre P. | Archaea | 10.1155/2006/582916 | 2007 | | |
| Enzymology | Distribution and phylogenies of enzymes of the Embden-Meyerhof-Parnas pathway from archaea and hyperthermophilic bacteria support a gluconeogenic origin of metabolism. | Ronimus RS, Morgan HW. | Archaea | 10.1155/2003/162593 | 2003 | |
| Genetics | Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. | Makarova KS, Wolf YI, Forterre P, Prangishvili D, Krupovic M, Koonin EV. | Extremophiles | 10.1007/s00792-014-0672-7 | 2014 | |
| Structure of a membrane-embedded prenyltransferase homologous to UBIAD1. | Huang H, Levin EJ, Liu S, Bai Y, Lockless SW, Zhou M. | PLoS Biol | 10.1371/journal.pbio.1001911 | 2014 | | |
| Genetics | Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome. | Okamoto A, Yamada K. | BMC Microbiol | 10.1186/1471-2180-11-249 | 2011 | |
| Metabolism | Morphology, biophysical properties and protein-mediated fusion of archaeosomes. | Sustar V, Zelko J, Lopalco P, Lobasso S, Ota A, Poklar Ulrih N, Corcelli A, Kralj-Iglic V. | PLoS One | 10.1371/journal.pone.0039401 | 2012 | |
| Genomic DNA k-mer spectra: models and modalities. | Chor B, Horn D, Goldman N, Levy Y, Massingham T. | Genome Biol | 10.1186/gb-2009-10-10-r108 | 2009 | | |
| Metabolism | Voltage-gated sodium channel (NaV) protein dissection creates a set of functional pore-only proteins. | Shaya D, Kreir M, Robbins RA, Wong S, Hammon J, Bruggemann A, Minor DL. | Proc Natl Acad Sci U S A | 10.1073/pnas.1106811108 | 2011 | |
| Enzymology | A broad specificity nucleoside kinase from Thermoplasma acidophilum. | Elkin SR, Kumar A, Price CW, Columbus L. | Proteins | 10.1002/prot.24212 | 2013 | |
| Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus. | Micorescu M, Grunberg S, Franke A, Cramer P, Thomm M, Bartlett M. | J Bacteriol | 10.1128/jb.01498-07 | 2008 | | |
| Metabolism | The Mus81-Mms4 structure-selective endonuclease requires nicked DNA junctions to undergo conformational changes and bend its DNA substrates for cleavage. | Mukherjee S, Wright WD, Ehmsen KT, Heyer WD. | Nucleic Acids Res | 10.1093/nar/gku265 | 2014 | |
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| Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis. | Kletzin A, Heimerl T, Flechsler J, van Niftrik L, Rachel R, Klingl A. | Front Microbiol | 10.3389/fmicb.2015.00439 | 2015 | | |
| Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP. | Butterwick JA, MacKinnon R. | J Mol Biol | 10.1016/j.jmb.2010.09.012 | 2010 | | |
| Cross-strand disulfides in the hydrogen bonding site of antiparallel beta-sheet (aCSDhs): Forbidden disulfides that are highly strained, easily broken. | Haworth NL, Wouters MJ, Hunter MO, Ma L, Wouters MA. | Protein Sci | 10.1002/pro.3545 | 2019 | | |
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| Metabolism | Kinetic and thermodynamic features reveal that Escherichia coli BCP is an unusually versatile peroxiredoxin. | Reeves SA, Parsonage D, Nelson KJ, Poole LB. | Biochemistry | 10.1021/bi200935d | 2011 | |
| Purine biosynthesis in archaea: variations on a theme. | Brown AM, Hoopes SL, White RH, Sarisky CA. | Biol Direct | 10.1186/1745-6150-6-63 | 2011 | | |
| Metabolism | New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. | Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L. | Nucleic Acids Res | 10.1093/nar/gkq451 | 2010 | |
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| Metabolism | Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. | Yang H, Fitz-Gibbon S, Marcotte EM, Tai JH, Hyman EC, Miller JH. | J Bacteriol | 10.1128/jb.182.5.1272-1279.2000 | 2000 | |
| Metabolism | Crystal structure of Archaeoglobus fulgidus CTP:inositol-1-phosphate cytidylyltransferase, a key enzyme for di-myo-inositol-phosphate synthesis in (hyper)thermophiles. | Brito JA, Borges N, Vonrhein C, Santos H, Archer M. | J Bacteriol | 10.1128/jb.01543-10 | 2011 | |
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| Metabolism | Structural basis of thermal stability of the tungsten cofactor synthesis protein MoaB from Pyrococcus furiosus. | Havarushka N, Fischer-Schrader K, Lamkemeyer T, Schwarz G. | PLoS One | 10.1371/journal.pone.0086030 | 2014 | |
| Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes. | Meyer BH, Adam PS, Wagstaff BA, Kolyfetis GE, Probst AJ, Albers SV, Dorfmueller HC. | Elife | 10.7554/elife.67448 | 2022 | | |
| Metabolism | Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya. | Wardle J, Burgers PM, Cann IK, Darley K, Heslop P, Johansson E, Lin LJ, McGlynn P, Sanvoisin J, Stith CM, Connolly BA. | Nucleic Acids Res | 10.1093/nar/gkm1023 | 2008 | |
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| Multiple replication origins with diverse control mechanisms in Haloarcula hispanica. | Wu Z, Liu J, Yang H, Liu H, Xiang H. | Nucleic Acids Res | 10.1093/nar/gkt1214 | 2014 | | |
| Metabolism | A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A TOOL FOR REDOX REGULATION IN AN ANAEROBE. | Susanti D, Loganathan U, Mukhopadhyay B. | J Biol Chem | 10.1074/jbc.m116.750208 | 2016 | |
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| Metabolism | Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5-related N-acetyltransferase-like proteins. | Cort JR, Ramelot TA, Murray D, Acton TB, Ma LC, Xiao R, Montelione GT, Kennedy MA. | J Struct Funct Genomics | 10.1007/s10969-008-9041-z | 2008 | |
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| Participation of the S4 voltage sensor in the Mg2+-dependent activation of large conductance (BK) K+ channels. | Hu L, Shi J, Ma Z, Krishnamoorthy G, Sieling F, Zhang G, Horrigan FT, Cui J. | Proc Natl Acad Sci U S A | 10.1073/pnas.1834300100 | 2003 | | |
| Multiple DNA binding domains mediate the function of the ERCC1-XPF protein in nucleotide excision repair. | Su Y, Orelli B, Madireddy A, Niedernhofer LJ, Scharer OD. | J Biol Chem | 10.1074/jbc.m111.337899 | 2012 | | |
| Time-shared experiments for efficient assignment of triple-selectively labeled proteins. | Lohr F, Laguerre A, Bock C, Reckel S, Connolly PJ, Abdul-Manan N, Tumulka F, Abele R, Moore JM, Dotsch V. | J Magn Reson | 10.1016/j.jmr.2014.09.014 | 2014 | | |
| Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family. | Oswal N, Sahni NS, Bhattacharya A, Komath SS, Muthuswami R. | BMC Evol Biol | 10.1186/1471-2148-8-168 | 2008 | | |
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| Metabolism | Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. | Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crecy-Lagard V. | ACS Chem Biol | 10.1021/cb500278k | 2014 | |
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| Nitrite-reductase and peroxynitrite isomerization activities of Methanosarcina acetivorans protoglobin. | Ascenzi P, Leboffe L, Pesce A, Ciaccio C, Sbardella D, Bolognesi M, Coletta M. | PLoS One | 10.1371/journal.pone.0095391 | 2014 | | |
| Enigmatic, ultrasmall, uncultivated Archaea. | Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF. | Proc Natl Acad Sci U S A | 10.1073/pnas.0914470107 | 2010 | | |
| Pathogenicity | Molecular determinants of KCNQ (Kv7) K+ channel sensitivity to the anticonvulsant retigabine. | Schenzer A, Friedrich T, Pusch M, Saftig P, Jentsch TJ, Grotzinger J, Schwake M. | J Neurosci | 10.1523/jneurosci.0128-05.2005 | 2005 | |
| Genetics | A conserved MCM single-stranded DNA binding element is essential for replication initiation. | Froelich CA, Kang S, Epling LB, Bell SP, Enemark EJ. | Elife | 10.7554/elife.01993 | 2014 | |
| Structural characterization of the voltage-sensor domain and voltage-gated K+-channel proteins vectorially oriented within a single bilayer membrane at the solid/vapor and solid/liquid interfaces via neutron interferometry. | Gupta S, Dura JA, Freites JA, Tobias DJ, Blasie JK. | Langmuir | 10.1021/la301219z | 2012 | | |
| Evaluating the efficacy of tryptophan fluorescence and absorbance as a selection tool for identifying protein crystals. | Gill HS. | Acta Crystallogr Sect F Struct Biol Cryst Commun | 10.1107/s1744309110002022 | 2010 | | |
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| Metabolism | Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea. | Li J, Zheng X, Guo X, Qi L, Dong X. | PLoS One | 10.1371/journal.pone.0095502 | 2014 | |
| Enzymology | Cloning and characterization of a family B DNA polymerase from the hyperthermophilic crenarchaeon Pyrobaculum islandicum. | Kahler M, Antranikian G. | J Bacteriol | 10.1128/jb.182.3.655-663.2000 | 2000 | |
| Metabolism | Activity and transcriptional regulation of bacterial protein-like glycerol-3-phosphate dehydrogenase of the haloarchaea in Haloferax volcanii. | Rawls KS, Martin JH, Maupin-Furlow JA. | J Bacteriol | 10.1128/jb.00276-11 | 2011 | |
| Metabolism | The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus. | Prunetti L, Brugna M, Lebrun R, Giudici-Orticoni MT, Guiral M. | PLoS One | 10.1371/journal.pone.0021616 | 2011 | |
| Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time. | Blank CE. | Archaea | 10.1155/2012/843539 | 2012 | | |
| Genetics | Lineage-specific gene expansions in bacterial and archaeal genomes. | Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV. | Genome Res | 10.1101/gr.gr-1660r | 2001 | |
| Voltage-dependent conformational changes of KVAP S4 segment in bacterial membrane environment. | Koag MC, Papazian DM. | Channels (Austin) | 10.4161/chan.3.5.9697 | 2009 | | |
| Metabolism | Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. | Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S. | Biochemistry | 10.1021/acs.biochem.7b00446 | 2017 | |
| The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T). | Manzella MP, Holmes DE, Rocheleau JM, Chung A, Reguera G, Kashefi K. | Stand Genomic Sci | 10.1186/s40793-015-0035-8 | 2015 | | |
| High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers. | Doherty T, Su Y, Hong M. | J Mol Biol | 10.1016/j.jmb.2010.06.048 | 2010 | | |
| Enzymology | Modelling the evolution of the archeal tryptophan synthase. | Merkl R. | BMC Evol Biol | 10.1186/1471-2148-7-59 | 2007 | |
| An analysis of amino acid sequences surrounding archaeal glycoprotein sequons. | Abu-Qarn M, Eichler J. | Archaea | 10.1155/2006/510578 | 2007 | | |
| Metabolism | A unique insert of leucyl-tRNA synthetase is required for aminoacylation and not amino acid editing. | Vu MT, Martinis SA. | Biochemistry | 10.1021/bi062078j | 2007 | |
| Metabolism | GO4genome: a prokaryotic phylogeny based on genome organization. | Merkl R, Wiezer A. | J Mol Evol | 10.1007/s00239-009-9233-6 | 2009 | |
| Enzymology | Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus. | Kiyonari S, Tahara S, Shirai T, Iwai S, Ishino S, Ishino Y. | Nucleic Acids Res | 10.1093/nar/gkp720 | 2009 | |
| Enzymology | The complex structures of isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila suggest a new active site locking mechanism. | Leiros HK, Fedoy AE, Leiros I, Steen IH. | FEBS Open Bio | 10.1016/j.fob.2012.06.003 | 2012 | |
| SIGI: score-based identification of genomic islands. | Merkl R. | BMC Bioinformatics | 10.1186/1471-2105-5-22 | 2004 | | |
| Metabolism | Structural basis for catalysis at the membrane-water interface. | Dufrisne MB, Petrou VI, Clarke OB, Mancia F. | Biochim Biophys Acta Mol Cell Biol Lipids | 10.1016/j.bbalip.2016.11.011 | 2017 | |
| Metabolism | Molecular determinants of origin discrimination by Orc1 initiators in archaea. | Dueber EC, Costa A, Corn JE, Bell SD, Berger JM. | Nucleic Acids Res | 10.1093/nar/gkq1308 | 2011 | |
| Metabolism | A domain for editing by an archaebacterial tRNA synthetase. | Beebe K, Merriman E, Ribas De Pouplana L, Schimmel P. | Proc Natl Acad Sci U S A | 10.1073/pnas.0401530101 | 2004 | |
| Metabolism | Reconstruction of the archaeal isoprenoid ether lipid biosynthesis pathway in Escherichia coli through digeranylgeranylglyceryl phosphate. | Lai D, Lluncor B, Schroder I, Gunsalus RP, Liao JC, Monbouquette HG. | Metab Eng | 10.1016/j.ymben.2009.01.008 | 2009 | |
| Genetics | Analysis of the crystal structure of an active MCM hexamer. | Miller JM, Arachea BT, Epling LB, Enemark EJ. | Elife | 10.7554/elife.03433 | 2014 | |
| Genetics | Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. | Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. | BMC Genomics | 10.1186/1471-2164-14-485 | 2013 | |
| Metabolism | Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. | Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG. | J Bacteriol | 10.1128/jb.01525-08 | 2009 | |
| Metabolism | Uncovering the human methyltransferasome. | Petrossian TC, Clarke SG. | Mol Cell Proteomics | 10.1074/mcp.m110.000976 | 2011 | |
| Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea. | Toffano-Nioche C, Gautheret D, Leclerc F. | Nucleic Acids Res | 10.1093/nar/gkv756 | 2015 | | |
| Genetics | Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes. | Tripathi LP, Sowdhamini R. | BMC Genomics | 10.1186/1471-2164-9-549 | 2008 | |
| Phylogeny | A phylogenomic profile of globins. | Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Gough J, Dewilde S, Moens L, Vanfleteren JR. | BMC Evol Biol | 10.1186/1471-2148-6-31 | 2006 | |
| Phylogeny | Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. | Beja O, Koonin EV, Aravind L, Taylor LT, Seitz H, Stein JL, Bensen DC, Feldman RA, Swanson RV, DeLong EF. | Appl Environ Microbiol | 10.1128/aem.68.1.335-345.2002 | 2002 | |
| Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. | Tsodikov OV, Ivanov D, Orelli B, Staresincic L, Shoshani I, Oberman R, Scharer OD, Wagner G, Ellenberger T. | EMBO J | 10.1038/sj.emboj.7601894 | 2007 | | |
| Metabolism | A novel biosynthetic pathway of archaetidyl-myo-inositol via archaetidyl-myo-inositol phosphate from CDP-archaeol and D-glucose 6-phosphate in methanoarchaeon Methanothermobacter thermautotrophicus cells. | Morii H, Kiyonari S, Ishino Y, Koga Y. | J Biol Chem | 10.1074/jbc.m109.034652 | 2009 | |
| A genetic approach for analyzing the co-operative function of the tRNA mimicry complex, eRF1/eRF3, in translation termination on the ribosome. | Wada M, Ito K. | Nucleic Acids Res | 10.1093/nar/gku493 | 2014 | | |
| Metabolism | Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. | Anantharaman V, Iyer LM, Aravind L. | Biol Direct | 10.1186/1745-6150-5-43 | 2010 | |
| Genetics | Applying negative rule mining to improve genome annotation. | Artamonova II, Frishman G, Frishman D. | BMC Bioinformatics | 10.1186/1471-2105-8-261 | 2007 | |
| Metabolism | Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales. | Paytubi S, McMahon SA, Graham S, Liu H, Botting CH, Makarova KS, Koonin EV, Naismith JH, White MF. | Proc Natl Acad Sci U S A | 10.1073/pnas.1113277108 | 2012 | |
| Metabolism | New insights on the mechanism of the K(+-) independent activity of crenarchaeota pyruvate kinases. | De la Vega-Ruiz G, Dominguez-Ramirez L, Riveros-Rosas H, Guerrero-Mendiola C, Torres-Larios A, Hernandez-Alcantara G, Garcia-Trejo JJ, Ramirez-Silva L. | PLoS One | 10.1371/journal.pone.0119233 | 2015 | |
| Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. | Makarova KS, Ponomarev VA, Koonin EV. | Genome Biol | 10.1186/gb-2001-2-9-research0033 | 2001 | | |
| Metabolism | Molecular template for a voltage sensor in a novel K+ channel. III. Functional reconstitution of a sensorless pore module from a prokaryotic Kv channel. | Santos JS, Grigoriev SM, Montal M. | J Gen Physiol | 10.1085/jgp.200810077 | 2008 | |
| Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment. | Lohr F, Reckel S, Karbyshev M, Connolly PJ, Abdul-Manan N, Bernhard F, Moore JM, Dotsch V. | J Biomol NMR | 10.1007/s10858-012-9601-1 | 2012 | | |
| Genetics | Fine-structured multi-scaling long-range correlations in completely sequenced genomes--features, origin, and classification. | Knoch TA, Goker M, Lohner R, Abuseiris A, Grosveld FG. | Eur Biophys J | 10.1007/s00249-009-0489-y | 2009 | |
| Metabolism | Functional characterization of the vitamin K2 biosynthetic enzyme UBIAD1. | Hirota Y, Nakagawa K, Sawada N, Okuda N, Suhara Y, Uchino Y, Kimoto T, Funahashi N, Kamao M, Tsugawa N, Okano T. | PLoS One | 10.1371/journal.pone.0125737 | 2015 | |
| Metabolism | Aminoacyl-tRNA-charged eukaryotic elongation factor 1A is the bona fide substrate for Legionella pneumophila effector glucosyltransferases. | Tzivelekidis T, Jank T, Pohl C, Schlosser A, Rospert S, Knudsen CR, Rodnina MV, Belyi Y, Aktories K. | PLoS One | 10.1371/journal.pone.0029525 | 2011 | |
| Genetics | Lineage-specific partitions in archaeal transcription. | Coulson RM, Touboul N, Ouzounis CA. | Archaea | 10.1155/2006/629868 | 2007 | |
| Metabolism | A highly selective oligopeptide binding protein from the archaeon Sulfolobus solfataricus. | Gogliettino M, Balestrieri M, Pocsfalvi G, Fiume I, Natale L, Rossi M, Palmieri G. | J Bacteriol | 10.1128/jb.01414-09 | 2010 | |
| Genetics | GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. | Besemer J, Lomsadze A, Borodovsky M. | Nucleic Acids Res | 10.1093/nar/29.12.2607 | 2001 | |
| Metabolism | Characterization of a heme-dependent catalase from Methanobrevibacter arboriphilus. | Shima S, Sordel-Klippert M, Brioukhanov A, Netrusov A, Linder D, Thauer RK. | Appl Environ Microbiol | 10.1128/aem.67.7.3041-3045.2001 | 2001 | |
| Metabolism | Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. | Matsunaga F, Glatigny A, Mucchielli-Giorgi MH, Agier N, Delacroix H, Marisa L, Durosay P, Ishino Y, Aggerbeck L, Forterre P. | Nucleic Acids Res | 10.1093/nar/gkm212 | 2007 | |
| Cross-reactivity of peanut allergens. | Bublin M, Breiteneder H. | Curr Allergy Asthma Rep | 10.1007/s11882-014-0426-8 | 2014 | | |
| Metabolism | A gating model for the archeal voltage-dependent K(+) channel KvAP in DPhPC and POPE:POPG decane lipid bilayers. | Schmidt D, Cross SR, MacKinnon R. | J Mol Biol | 10.1016/j.jmb.2009.05.062 | 2009 | |
| Metabolism | The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves. | Randau L, Calvin K, Hall M, Yuan J, Podar M, Li H, Soll D. | Proc Natl Acad Sci U S A | 10.1073/pnas.0509197102 | 2005 | |
| Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. | Jeudy S, Abergel C, Claverie JM, Legendre M. | PLoS Genet | 10.1371/journal.pgen.1003122 | 2012 | | |
| Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters. | Wang J, Dasgupta I, Fox GE. | Archaea | 10.1155/2009/971494 | 2009 | | |
| Phylogeny | Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage. | Song J, Xu Q, Olsen R, Loomis WF, Shaulsky G, Kuspa A, Sucgang R. | PLoS Comput Biol | 10.1371/journal.pcbi.0010071 | 2005 | |
| Membrane protein prediction methods. | Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B. | Methods | 10.1016/j.ymeth.2006.07.026 | 2007 | | |
| Metabolism | Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. | Menezes S, Gaston KW, Krivos KL, Apolinario EE, Reich NO, Sowers KR, Limbach PA, Perona JJ. | Nucleic Acids Res | 10.1093/nar/gkr475 | 2011 | |
| Metabolism | PCNA and XPF cooperate to distort DNA substrates. | Hutton RD, Craggs TD, White MF, Penedo JC. | Nucleic Acids Res | 10.1093/nar/gkp1104 | 2010 | |
| Archaeal signal peptides--a comparative survey at the genome level. | Bardy SL, Eichler J, Jarrell KF. | Protein Sci | 10.1110/ps.03148703 | 2003 | | |
| Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications. | Shaul S, Berel D, Benjamini Y, Graur D. | RNA | 10.1261/rna.1745910 | 2010 | | |
| Metabolism | A transposon-derived DNA polymerase from Entamoeba histolytica displays intrinsic strand displacement, processivity and lesion bypass. | Pastor-Palacios G, Lopez-Ramirez V, Cardona-Felix CS, Brieba LG. | PLoS One | 10.1371/journal.pone.0049964 | 2012 | |
| Molecular modeling of the bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase and predictions of structural effects of mutations associated with HIBM and sialuria. | Kurochkina N, Yardeni T, Huizing M. | Glycobiology | 10.1093/glycob/cwp176 | 2010 | | |
| Phylogeny | The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. | McCann A, Cotton JA, McInerney JO. | BMC Evol Biol | 10.1186/1471-2148-8-312 | 2008 | |
| Phylogeny | In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership. | Jako E, Ittzes P, Szenes A, Kun A, Szathmary E, Pal G. | Nucleic Acids Res | 10.1093/nar/gkm598 | 2007 | |
| Enzymology | Characterization of a zinc-containing alcohol dehydrogenase with stereoselectivity from the hyperthermophilic archaeon Thermococcus guaymasensis. | Ying X, Ma K. | J Bacteriol | 10.1128/jb.01433-10 | 2011 | |
| Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures. | Pride DT, Schoenfeld T. | BMC Genomics | 10.1186/1471-2164-9-420 | 2008 | | |
| Metabolism | Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. | Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR. | PLoS One | 10.1371/journal.pone.0016626 | 2011 | |
| Enzymology | Identification of an alternative nucleoside triphosphate: 5'-deoxyadenosylcobinamide phosphate nucleotidyltransferase in Methanobacterium thermoautotrophicum delta H. | Thomas MG, Escalante-Semerena JC. | J Bacteriol | 10.1128/jb.182.15.4227-4233.2000 | 2000 | |
| Metabolism | Bacillus subtilis GlcK activity requires cysteines within a motif that discriminates microbial glucokinases into two lineages. | Mesak LR, Mesak FM, Dahl MK. | BMC Microbiol | 10.1186/1471-2180-4-6 | 2004 | |
| Metabolism | Molecular analyses of a three-subunit euryarchaeal clamp loader complex from Methanosarcina acetivorans. | Chen YH, Lin Y, Yoshinaga A, Chhotani B, Lorenzini JL, Crofts AA, Mei S, Mackie RI, Ishino Y, Cann IK. | J Bacteriol | 10.1128/jb.00414-09 | 2009 | |
| Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization. | Tripsianes K, Folkers GE, Zheng C, Das D, Grinstead JS, Kaptein R, Boelens R. | Nucleic Acids Res | 10.1093/nar/gkm503 | 2007 | | |
| Metabolism | The human Kv1.1 channel is palmitoylated, modulating voltage sensing: Identification of a palmitoylation consensus sequence. | Gubitosi-Klug RA, Mancuso DJ, Gross RW. | Proc Natl Acad Sci U S A | 10.1073/pnas.0501999102 | 2005 | |
| ProtRepeatsDB: a database of amino acid repeats in genomes. | Kalita MK, Ramasamy G, Duraisamy S, Chauhan VS, Gupta D. | BMC Bioinformatics | 10.1186/1471-2105-7-336 | 2006 | | |
| Molecular architecture and divalent cation activation of TvoK, a prokaryotic potassium channel. | Parfenova LV, Abarca-Heidemann K, Crane BM, Rothberg BS. | J Biol Chem | 10.1074/jbc.m703650200 | 2007 | | |
| bSUM: A bead-supported unilamellar membrane system facilitating unidirectional insertion of membrane proteins into giant vesicles. | Zheng H, Lee S, Llaguno MC, Jiang QX. | J Gen Physiol | 10.1085/jgp.201511448 | 2016 | | |
| Enzymology | Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms. | Shaul S, Nussinov R, Pupko T. | BMC Evol Biol | 10.1186/1471-2148-6-22 | 2006 | |
| Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes. | Wilson GA, Feil EJ, Lilley AK, Field D. | PLoS One | 10.1371/journal.pone.0000324 | 2007 | | |
| Evolution of gene fusions: horizontal transfer versus independent events. | Yanai I, Wolf YI, Koonin EV. | Genome Biol | 10.1186/gb-2002-3-5-research0024 | 2002 | | |
| Metabolism | An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA. | Haseltine CA, Kowalczykowski SC. | Nucleic Acids Res | 10.1093/nar/gkp068 | 2009 | |
| Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases. | Chandrasekaran SN, Yardimci GG, Erdogan O, Roach J, Carter CW. | Mol Biol Evol | 10.1093/molbev/mst070 | 2013 | | |
| Metabolism | Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. | Pierce E, Becker DF, Ragsdale SW. | J Biol Chem | 10.1074/jbc.m110.155739 | 2010 | |
| A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. | Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. | Genome Biol | 10.1186/gb-2008-9-11-r158 | 2008 | | |
| Enzymology | The emerging periplasm-localized subclass of AroQ chorismate mutases, exemplified by those from Salmonella typhimurium and Pseudomonas aeruginosa. | Calhoun DH, Bonner CA, Gu W, Xie G, Jensen RA. | Genome Biol | 10.1186/gb-2001-2-8-research0030 | 2001 | |
| Metabolism | Gating of the bacterial sodium channel, NaChBac: voltage-dependent charge movement and gating currents. | Kuzmenkin A, Bezanilla F, Correa AM. | J Gen Physiol | 10.1085/jgp.200409139 | 2004 | |
| Enzymology | Arsenite oxidase aox genes from a metal-resistant beta-proteobacterium. | Muller D, Lievremont D, Simeonova DD, Hubert JC, Lett MC. | J Bacteriol | 10.1128/jb.185.1.135-141.2003 | 2003 | |
| Genetics | Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. | Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N. | J Bacteriol | 10.1128/jb.01949-07 | 2008 | |
| The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. | Iyer LM, Aravind L. | BMC Genomics | 10.1186/1471-2164-3-33 | 2002 | | |
| The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn. | Nolivos S, Carpousis AJ, Clouet-d'Orval B. | Nucleic Acids Res | 10.1093/nar/gki962 | 2005 | | |
| Metabolism | Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis. | Aravind L, de Souza RF, Iyer LM. | Biol Direct | 10.1186/1745-6150-5-48 | 2010 | |
| Metabolism | The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein. | Fenyk S, Townsend PD, Dixon CH, Spies GB, de San Eustaquio Campillo A, Slootweg EJ, Westerhof LB, Gawehns FK, Knight MR, Sharples GJ, Goverse A, Palsson LO, Takken FL, Cann MJ. | J Biol Chem | 10.1074/jbc.m115.672121 | 2015 | |
| Metabolism | Biosynthesis of ubiquinone compounds with conjugated prenyl side chains. | Lee PC, Salomon C, Mijts B, Schmidt-Dannert C. | Appl Environ Microbiol | 10.1128/aem.01495-08 | 2008 | |
| Metabolism | Acylpeptide hydrolase inhibition as targeted strategy to induce proteasomal down-regulation. | Palmieri G, Bergamo P, Luini A, Ruvo M, Gogliettino M, Langella E, Saviano M, Hegde RN, Sandomenico A, Rossi M. | PLoS One | 10.1371/journal.pone.0025888 | 2011 | |
| Metabolism | Characterization of two methanopterin biosynthesis mutants of Methylobacterium extorquens AM1 by use of a tetrahydromethanopterin bioassay. | Rasche ME, Havemann SA, Rosenzvaig M. | J Bacteriol | 10.1128/jb.186.5.1565-1570.2004 | 2004 | |
| Phylogeny | Visualization of the phylogenetic content of five genomes using dekapentagonal maps. | Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP. | Genome Biol | 10.1186/gb-2004-5-3-r20 | 2004 | |
| Bacterial regulatory networks are extremely flexible in evolution. | Lozada-Chavez I, Janga SC, Collado-Vides J. | Nucleic Acids Res | 10.1093/nar/gkl423 | 2006 | | |
| Metabolism | Generation, comparison, and merging of pathways between protein conformations: gating in K-channels. | Enosh A, Raveh B, Furman-Schueler O, Halperin D, Ben-Tal N. | Biophys J | 10.1529/biophysj.108.135285 | 2008 | |
| Domain architecture conservation in orthologs. | Forslund K, Pekkari I, Sonnhammer EL. | BMC Bioinformatics | 10.1186/1471-2105-12-326 | 2011 | | |
| Enzymology | The structure of an archaeal homodimeric ligase which has RNA circularization activity. | Brooks MA, Meslet-Cladiere L, Graille M, Kuhn J, Blondeau K, Myllykallio H, van Tilbeurgh H. | Protein Sci | 10.1110/ps.035493.108 | 2008 | |
| Genetics | An improved probability mapping approach to assess genome mosaicism. | Zhaxybayeva O, Gogarten JP. | BMC Genomics | 10.1186/1471-2164-4-37 | 2003 | |
| Metabolism | Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. | Li Z, Lu S, Hou G, Ma X, Sheng D, Ni J, Shen Y. | J Bacteriol | 10.1128/jb.01662-07 | 2008 | |
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| A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. | Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y. | Proc Natl Acad Sci U S A | 10.1073/pnas.96.16.8873 | 1999 | | |
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| Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. | Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. | Genome Res | 10.1101/gr.1993504 | 2004 | | |
| Genetics | A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. | Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV. | Nucleic Acids Res | 10.1093/nar/30.2.482 | 2002 | |
| Metabolism | Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity. | Inagaki Y, Blouin C, Doolittle WF, Roger AJ. | Nucleic Acids Res | 10.1093/nar/30.2.532 | 2002 | |
| A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. | Galperin MY. | BMC Microbiol | 10.1186/1471-2180-5-35 | 2005 | | |
| Metabolism | Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. | Clouet d'Orval B, Bortolin ML, Gaspin C, Bachellerie JP. | Nucleic Acids Res | 10.1093/nar/29.22.4518 | 2001 | |
| A homology model of the pore region of HCN channels. | Giorgetti A, Carloni P, Mistrik P, Torre V. | Biophys J | 10.1529/biophysj.104.045286 | 2005 | | |
| Metabolism | Conversion of methionine to cysteine in Bacillus subtilis and its regulation. | Hullo MF, Auger S, Soutourina O, Barzu O, Yvon M, Danchin A, Martin-Verstraete I. | J Bacteriol | 10.1128/jb.01273-06 | 2007 | |
| Genetics | Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. | Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T. | Genome Res | 10.1101/gr.3003105 | 2005 | |
| Metabolism | Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus. | Cann IK, Ishino S, Yuasa M, Daiyasu H, Toh H, Ishino Y. | J Bacteriol | 10.1128/jb.183.8.2614-2623.2001 | 2001 | |
| The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. | Gonzalez V, Bustos P, Ramirez-Romero MA, Medrano-Soto A, Salgado H, Hernandez-Gonzalez I, Hernandez-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodriguez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, Davila G. | Genome Biol | 10.1186/gb-2003-4-6-r36 | 2003 | | |
| Coupled motions between pore and voltage-sensor domains: a model for Shaker B, a voltage-gated potassium channel. | Treptow W, Maigret B, Chipot C, Tarek M. | Biophys J | 10.1529/biophysj.104.039628 | 2004 | | |
| Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. | Mazumder R, Iyer LM, Vasudevan S, Aravind L. | Nucleic Acids Res | 10.1093/nar/gkf645 | 2002 | | |
| PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. | Neuwald AF, Poleksic A. | Nucleic Acids Res | 10.1093/nar/28.18.3570 | 2000 | | |
| Phylogeny | Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria. | Watanabe Y, Gray MW. | Nucleic Acids Res | 10.1093/nar/28.12.2342 | 2000 | |
| Metabolism | Functional interactions of a homolog of proliferating cell nuclear antigen with DNA polymerases in Archaea. | Cann IK, Ishino S, Hayashi I, Komori K, Toh H, Morikawa K, Ishino Y. | J Bacteriol | 10.1128/jb.181.21.6591-6599.1999 | 1999 | |
| Electrostatic model of S4 motion in voltage-gated ion channels. | Lecar H, Larsson HP, Grabe M. | Biophys J | 10.1016/s0006-3495(03)74708-0 | 2003 | | |
| Genetics | A complete sequence of the T. tengcongensis genome. | Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H. | Genome Res | 10.1101/gr.219302 | 2002 | |
| An inventory of yeast proteins associated with nucleolar and ribosomal components. | Staub E, Mackowiak S, Vingron M. | Genome Biol | 10.1186/gb-2006-7-10-r98 | 2006 | | |
| Structural characterization of the human proteome. | Muller A, MacCallum RM, Sternberg MJ. | Genome Res | 10.1101/gr.221202 | 2002 | | |
| Genetics | A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. | Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM. | Elife | 10.7554/elife.00882 | 2013 | |
| Biosynthesis and role of N-linked glycosylation in cell surface structures of archaea with a focus on flagella and s layers. | Jarrell KF, Jones GM, Nair DB. | Int J Microbiol | 10.1155/2010/470138 | 2010 | | |
| SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. | Aravind L, Makarova KS, Koonin EV. | Nucleic Acids Res | 10.1093/nar/28.18.3417 | 2000 | | |
| Phylogeny | Genome trees constructed using five different approaches suggest new major bacterial clades. | Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV. | BMC Evol Biol | 10.1186/1471-2148-1-8 | 2001 | |
| Metabolism | The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. | Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK. | J Bacteriol | 10.1128/jb.188.2.642-658.2006 | 2006 | |
| Metabolism | Chemoenzymatic Semisynthesis of Proteins. | Thompson RE, Muir TW. | Chem Rev | 10.1021/acs.chemrev.9b00450 | 2020 | |
| Metabolism | Aminoacyl-tRNA Synthetases in the Bacterial World. | Giege R, Springer M. | EcoSal Plus | 10.1128/ecosalplus.esp-0002-2016 | 2016 | |
| Metabolism | Comparative genomics and evolution of proteins involved in RNA metabolism. | Anantharaman V, Koonin EV, Aravind L. | Nucleic Acids Res | 10.1093/nar/30.7.1427 | 2002 | |
| Metabolism | Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. | Brasen C, Esser D, Rauch B, Siebers B. | Microbiol Mol Biol Rev | 10.1128/mmbr.00041-13 | 2014 | |
| Molecular diversity and regulation of renal potassium channels. | Hebert SC, Desir G, Giebisch G, Wang W. | Physiol Rev | 10.1152/physrev.00051.2003 | 2005 | | |
| Enzymology | Kinetic study of sn-glycerol-1-phosphate dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix K1. | Han JS, Kosugi Y, Ishida H, Ishikawa K | Eur J Biochem | 10.1046/j.0014-2956.2001.02731.x | 2002 | |
| Enzymology | Glutamate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications. | Bhuiya MW, Sakuraba H, Kujo C, Nunoura-Kominato N, Kawarabayasi Y, Kikuchi H, Ohshima T | Extremophiles | 10.1007/s007920070002 | 2000 | |
| Enzymology | Purification and characterization of an intracellular heat-stable proteinase (pernilase) from the marine hyperthermophilic archaeon Aeropyrum pernix K1. | Chavez Croocker P, Sako Y, Uchida A | Extremophiles | 10.1007/s007920050093 | 1999 | |
| Enzymology | An extremely heat-stable extracellular proteinase (aeropyrolysin) from the hyperthermophilic archaeon Aeropyrum pernix K1. | Sako Y, Croocker PC, Ishida Y | FEBS Lett | 10.1016/s0014-5793(97)01153-8 | 1997 | |
| Pyrobaculum calidifontis sp. nov., a novel hyperthermophilic archaeon that grows in atmospheric air. | Amo T, Paje ML, Inagaki A, Ezaki S, Atomi H, Imanaka T. | Archaea | 10.1155/2002/616075 | 2002 | | |
| Phylogeny | Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees C. | Sako Y, Nomura N, Uchida A, Ishida Y, Morii H, Koga Y, Hoaki T, Maruyama T | Int J Syst Bacteriol | 10.1099/00207713-46-4-1070 | 1996 | |
How to citeIf you want to cite this particular strain cite the following doi:
https://doi.org/10.13145/bacdive4195.20251217.10
When using BacDive for research please cite the following paper
BacDive in 2025: the core database for prokaryotic strain data
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