archaeal proteins

Summary

Summary: Proteins found in any species of archaeon.

Top Publications

  1. Driessen R, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar U, et al. Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends. Nucleic Acids Res. 2013;41:196-205 pubmed publisher
    ..Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein-DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins. ..
  2. Desai K, Bingman C, Phillips G, Raines R. Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation. Biochemistry. 2013;52:2518-25 pubmed publisher
  3. Pan M, Santangelo T, Cubonová L, Li Z, Metangmo H, Ladner J, et al. Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability. Extremophiles. 2013;17:453-61 pubmed publisher
    ..kodakarensis strain with TK0535 (PCNA1) deleted were unsuccessful. The implications of these observations for PCNA1 function and the origin of the two PCNA-encoding genes in T. kodakarensis are discussed. ..
  4. Lassak K, Peeters E, Wrobel S, Albers S. The one-component system ArnR: a membrane-bound activator of the crenarchaeal archaellum. Mol Microbiol. 2013;88:125-39 pubmed publisher
    ..Finally, bioinformatic analysis revealed ArnR to be conserved not only in Sulfolobales but also in the crenarchaeal order of Desulfurococcales and thus might represent a more general control mechanism of archaeal motility...
  5. Pedro Roig L, Camacho M, Bonete M. Haloferax mediterranei GlnK proteins are post-translationally modified by uridylylation. Proteomics. 2013;13:1371-4 pubmed publisher
    ..mediterranei are post-translationally uridylylated. A third spot with lower pI suggests the existence of a non-descript post-translational modification in this protein family...
  6. Eichler J, Maupin Furlow J. Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea. FEMS Microbiol Rev. 2013;37:583-606 pubmed publisher
    ..In this review, recent developments concerning PTMs and protein degradation in the haloarchaea are discussed. ..
  7. Peng W, Li H, Hallstrøm S, Peng N, Liang Y, She Q. Genetic determinants of PAM-dependent DNA targeting and pre-crRNA processing in Sulfolobus islandicus. RNA Biol. 2013;10:738-48 pubmed publisher
    ..This demonstrates that in addition to Cas6, other Cas proteins of an archaeal type IA system also contribute to crRNA processing. ..
  8. Wang J, Fessl T, Schroeder K, Ouellet J, Liu Y, Freeman A, et al. Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein. Biophys J. 2012;103:2541-8 pubmed publisher
    ..The data support a passive conformational selection model by which the protein selects a fraction of RNA that is already in the kinked conformation, thereby drawing the equilibrium into this form...
  9. Kuba Y, Ishino S, Yamagami T, Tokuhara M, Kanai T, Fujikane R, et al. Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis. Genes Cells. 2012;17:923-37 pubmed publisher
    ..The sensitivities of the ?pcna2 mutant strain to ultraviolet irradiation (UV), methyl methanesulfonate (MMS) and mitomycin C (MMC) were indistinguishable from those of the wild-type strain. ..

More Information

Publications62

  1. Perrochia L, Guetta D, Hecker A, Forterre P, Basta T. Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification. Nucleic Acids Res. 2013;41:9484-99 pubmed publisher
    ..Overall, our data support a mechanistic model in which the final step in the biosynthesis of t(6)A relies on a strictly catalytic component, Kae1, and three partner proteins necessary for dimerization, tRNA binding and regulation...
  2. Cohen Rosenzweig C, Yurist Doutsch S, Eichler J. AglS, a novel component of the Haloferax volcanii N-glycosylation pathway, is a dolichol phosphate-mannose mannosyltransferase. J Bacteriol. 2012;194:6909-16 pubmed publisher
  3. Wang T, Sessions A, Lunde C, Rouhani S, Glaeser R, Duan Y, et al. Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway. Structure. 2013;21:290-7 pubmed publisher
    ..We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality. ..
  4. Samson R, Xu Y, Gadelha C, Stone T, Faqiri J, Li D, et al. Specificity and function of archaeal DNA replication initiator proteins. Cell Rep. 2013;3:485-96 pubmed publisher
    ..Finally, we reveal that ATP and DNA binding by Orc1-1 remodels the protein's structure rather than that of the DNA template. ..
  5. Li M, Liu H, Han J, Liu J, Wang R, Zhao D, et al. Characterization of CRISPR RNA biogenesis and Cas6 cleavage-mediated inhibition of a provirus in the haloarchaeon Haloferax mediterranei. J Bacteriol. 2013;195:867-75 pubmed publisher
    ..These results provide fundamental information for the subtype I-B CRISPR-Cas system in halophilic archaea and suggest diversified mechanisms and multiple physiological functions for the CRISPR-Cas system...
  6. Hou L, Klug G, Evguenieva Hackenberg E. The archaeal DnaG protein needs Csl4 for binding to the exosome and enhances its interaction with adenine-rich RNAs. RNA Biol. 2013;10:415-24 pubmed publisher
    ..solfataricus exosome. This apparently reflects the need for effective and selective recruitment of adenine-rich RNAs to the exosome in the RNA metabolism of S. solfataricus...
  7. Nyirenda J, Matsumoto S, Saitoh T, Maita N, Noda N, Inagaki F, et al. Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance. Structure. 2013;21:32-41 pubmed publisher
    ..These results suggest the necessity of multiple conformational states in the reaction. The dynamic nature of the Ser/Thr pocket could facilitate the efficient scanning of N-glycosylation sequons along nascent polypeptide chains...
  8. Deng L, Garrett R, Shah S, Peng X, She Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol Microbiol. 2013;87:1088-99 pubmed publisher
    ..islandicus REY15A which cooperate functionally by sharing a single Cas6 protein for crRNA processing and utilize crRNA products from identical CRISPR spacers. ..
  9. Krupovic M, Gonnet M, Hania W, Forterre P, Erauso G. Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids. PLoS ONE. 2013;8:e49044 pubmed publisher
    ..Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles...
  10. Ishibashi M, Hayashi T, Yoshida C, Tokunaga M. Increase of salt dependence of halophilic nucleoside diphosphate kinase caused by a single amino acid substitution. Extremophiles. 2013;17:585-91 pubmed publisher
    ..The results of this study help to elucidate the process for engineering industrial enzymes by controlling subunit-subunit interactions through mutations. ..
  11. Lange S, Alkhnbashi O, Rose D, Will S, Backofen R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 2013;41:8034-44 pubmed publisher
    ..informatik.uni-freiburg.de/CRISPRmap. ..
  12. Rouillon C, Zhou M, Zhang J, Politis A, Beilsten Edmands V, Cannone G, et al. Structure of the CRISPR interference complex CSM reveals key similarities with cascade. Mol Cell. 2013;52:124-34 pubmed publisher
    ..This reveals a three-dimensional model for the CSM complex that includes a helical component strikingly reminiscent of the backbone structure of the type I (Cascade) family. ..
  13. Stolboushkina E, Nikonov S, Zelinskaya N, Arkhipova V, Nikulin A, Garber M, et al. Crystal structure of the archaeal translation initiation factor 2 in complex with a GTP analogue and Met-tRNAf(Met.). J Mol Biol. 2013;425:989-98 pubmed publisher
    ..Remarkably, the recently published 5.0-Å-resolution structure of almost the same ternary initiation complex differs dramatically from the structure presented. Reasons for this discrepancy are discussed. ..
  14. Perrochia L, Crozat E, Hecker A, Zhang W, Bareille J, Collinet B, et al. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res. 2013;41:1953-64 pubmed publisher
    ..These findings shed light on the reaction mechanism of t(6)A synthesis and evolution of molecular systems that promote translation fidelity in present-day cells...
  15. Maupin Furlow J. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 2013;21:31-8 pubmed publisher
    ..These findings provide a new perspective on how Ubl proteins can serve as both sulfur carriers and protein modifiers in the absence of canonical E2 ubiquitin conjugating or E3 ubiquitin ligase enzyme homologs. ..
  16. Wolf Y, Makarova K, Yutin N, Koonin E. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct. 2012;7:46 pubmed publisher
    ..This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG). ..
  17. Phung D, Rinaldi D, Langendijk Genevaux P, Quentin Y, Carpousis A, Clouet d Orval B. Archaeal ?-CASP ribonucleases of the aCPSF1 family are orthologs of the eukaryal CPSF-73 factor. Nucleic Acids Res. 2013;41:1091-103 pubmed publisher
    ..Altogether, our results suggest that aCPSF1 performs an essential function and that an enzyme with similar activities was present in the last common ancestor of Archaea and Eukarya. ..
  18. Winter J, Bunting K. Rings in the extreme: PCNA interactions and adaptations in the archaea. Archaea. 2012;2012:951010 pubmed publisher
    Biochemical and structural analysis of archaeal proteins has enabled us to gain great insight into many eukaryotic processes, simultaneously offering fascinating glimpses into the adaptation and evolution of proteins at the extremes of ..
  19. Shao Y, Cocozaki A, Ramia N, Terns R, Terns M, Li H. Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex. Structure. 2013;21:376-84 pubmed publisher
    ..Further mutational analysis of the two conserved (but non-Cmr2-binding) glycine-rich loops of Cmr3 identified a region that is likely involved in assembly or the RNA cleavage function of the Cmr complex...
  20. Čuboňováa L, Katano M, Kanai T, Atomi H, Reeve J, Santangelo T. An archaeal histone is required for transformation of Thermococcus kodakarensis. J Bacteriol. 2012;194:6864-74 pubmed publisher
    ..Potential roles for the archaeal histones in regulating gene expression and for HTkA in DNA uptake and recombination are discussed. ..
  21. Podar M, Makarova K, Graham D, Wolf Y, Koonin E, Reysenbach A. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct. 2013;8:9 pubmed publisher
    ..A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes...
  22. Shao Y, Li H. Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6. Structure. 2013;21:385-93 pubmed
    ..The distinct RNA binding and cleavage mechanisms underline the diversity in CRISPR RNA processing. ..
  23. Reeks J, Sokolowski R, Graham S, Liu H, Naismith J, White M. Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing. Biochem J. 2013;452:223-30 pubmed publisher
  24. Reeks J, Graham S, Anderson L, Liu H, White M, Naismith J. Structure of the archaeal Cascade subunit Csa5: relating the small subunits of CRISPR effector complexes. RNA Biol. 2013;10:762-9 pubmed publisher
    ..A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes...
  25. Delmas S, Duggin I, Allers T. DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii. Mol Microbiol. 2013;87:168-79 pubmed publisher
  26. Pedro Roig L, Camacho M, Bonete M. Regulation of ammonium assimilation in Haloferax mediterranei: interaction between glutamine synthetase and two GlnK proteins. Biochim Biophys Acta. 2013;1834:16-23 pubmed publisher
    ..This protein-protein interaction increases glutamine synthetase activity in the presence of 2-oxoglutarate. Separate experiments that were carried out with GlnK(1) and GlnK(2) produced equivalent results...
  27. Littlechild J. Thermophilic archaeal enzymes and applications in biocatalysis. Biochem Soc Trans. 2011;39:155-8 pubmed publisher
    ..The L-2-haloacid dehalogenase has applications both in biocatalysis and in bioremediation. All of these enzymes have increased thermostability over their mesophilic counterparts...
  28. Kaminski L, Guan Z, Abu Qarn M, Konrad Z, Eichler J. AglR is required for addition of the final mannose residue of the N-linked glycan decorating the Haloferax volcanii S-layer glycoprotein. Biochim Biophys Acta. 2012;1820:1664-70 pubmed publisher
    ..Although roles have been assigned to the majority of Agl proteins, others await description. In the following, the contribution of AglR to N-glycosylation was addressed...
  29. Deng L, Kenchappa C, Peng X, She Q, Garrett R. Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res. 2012;40:2470-80 pubmed publisher
    ..Supporting evidence is provided by microarray and northern blotting analyses, and publicly available whole-transcriptome data for S. solfataricus P2. ..
  30. Lambrecht J, Flynn J, Downs D. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J Biol Chem. 2012;287:3454-61 pubmed publisher
    ..The conservation of the RidA/YjgF family suggests that reactive enamine/imine metabolites are of concern to all organisms...
  31. Beattie T, Bell S. Molecular machines in archaeal DNA replication. Curr Opin Chem Biol. 2011;15:614-9 pubmed publisher
    ..Although both complexes form ring shaped assemblies, they play very distinct roles at the leading and trailing edges of the replication fork machinery respectively. ..
  32. Igura M, Kohda D. Selective control of oligosaccharide transfer efficiency for the N-glycosylation sequon by a point mutation in oligosaccharyltransferase. J Biol Chem. 2011;286:13255-60 pubmed publisher
    ..This mutational approach is potentially applicable to eukaryotic and eubacterial OSTs for the production of homogenous glycoproteins in engineered mammalian and Escherichia coli cells. ..
  33. Samson R, Obita T, Hodgson B, Shaw M, Chong P, Williams R, et al. Molecular and structural basis of ESCRT-III recruitment to membranes during archaeal cell division. Mol Cell. 2011;41:186-96 pubmed publisher
    ..Furthermore, CdvA and ESCRT-III synergize to deform archaeal membranes in vitro. The structure of the CdvA/ESCRT-III interface gives insight into the evolution of the more complex and modular eukaryotic ESCRT complex...
  34. Liew L, Bell S. The interplay of DNA binding, ATP hydrolysis and helicase activities of the archaeal MCM helicase. Biochem J. 2011;436:409-14 pubmed publisher
    ..Our results identify a potential conduit for communicating DNA-binding information to the ATPase active site. ..
  35. Wojtas M, Peralta B, Ondiviela M, Mogni M, Bell S, Abrescia N. Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit. Biochem Soc Trans. 2011;39:25-30 pubmed publisher
  36. Ghosh A, Hartung S, van der Does C, Tainer J, Albers S. Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding. Biochem J. 2011;437:43-52 pubmed publisher
    ..The results of the present study report the first detailed biochemical analyses of the motor protein of an archaeal flagellum. ..
  37. Menezes S, Gaston K, Krivos K, Apolinario E, Reich N, Sowers K, et al. Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. Nucleic Acids Res. 2011;39:7641-55 pubmed publisher
    ..In the archaeal branch, the protein is found exclusively in thermophiles. More distantly related Trm14 homologs were also identified in eukaryotes known to possess the m(2)G6 tRNA modification...
  38. Sousa F, Alves R, Ribeiro M, Pereira Leal J, Teixeira M, Pereira M. The superfamily of heme-copper oxygen reductases: types and evolutionary considerations. Biochim Biophys Acta. 2012;1817:629-37 pubmed publisher
    ..We observed that HCOs are widely distributed in the two prokaryotic domains and that the different types of enzymes are not confined to a specific taxonomic group or environmental niche. ..
  39. Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin A. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 2011;30:4616-27 pubmed publisher
    ..Our studies suggest that the Cas3 HD nucleases working together with the Cas3 helicases can completely degrade invasive DNAs through the combination of endo- and exonuclease activities...
  40. Lassak K, Neiner T, Ghosh A, Klingl A, Wirth R, Albers S. Molecular analysis of the crenarchaeal flagellum. Mol Microbiol. 2012;83:110-24 pubmed publisher
    ..Electron micrographs demonstrated that lack of motility coincided with the loss of flagellar assembly. Thus we demonstrated that all seven fla genes are essential for crenarchaeal flagellum assembly and function...
  41. Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, et al. Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell. 2012;45:303-13 pubmed publisher
    ..Both target and guide RNAs can be cleaved, although a single molecule of guide RNA can support the degradation of multiple targets. ..
  42. Wang R, Zheng H, Preamplume G, Shao Y, Li H. The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex. Protein Sci. 2012;21:405-17 pubmed publisher
    ..Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state...
  43. Greber B, Boehringer D, Godinic Mikulcic V, Crnkovic A, Ibba M, Weygand Durasevic I, et al. Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. J Mol Biol. 2012;418:145-60 pubmed publisher
    ..The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea...
  44. Schmitt E, Panvert M, Lazennec Schurdevin C, Coureux P, Perez J, Thompson A, et al. Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA. Nat Struct Mol Biol. 2012;19:450-4 pubmed publisher
    ..We conclude that despite considerable structural homology between the core ? subunit of aIF2 and the elongation factor EF1A, these two G proteins of the translation apparatus use very different tRNA-binding strategies...
  45. Balasubramanian M, Srinivasan R, Huang Y, Ng K. Comparing contractile apparatus-driven cytokinesis mechanisms across kingdoms. Cytoskeleton (Hoboken). 2012;69:942-56 pubmed publisher
    ..Intriguingly, there are life forms on this planet that appear to lack molecules currently known to participate in cytokinesis and how these cells perform cytokinesis remains a mystery waiting to be unravelled...
  46. Haft D, Payne S, Selengut J. Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. J Bacteriol. 2012;194:36-48 pubmed publisher
    ..Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation. ..
  47. Skowyra A, MacNeill S. Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism. Nucleic Acids Res. 2012;40:1077-90 pubmed publisher
    ..Taken together, our results offer important insights into archaeal SSB function and establish the haloarchaea as a valuable model for further studies. ..
  48. Maier S, Schleberger P, Lu W, Wacker T, Pflüger T, Litz C, et al. Mechanism of disruption of the Amt-GlnK complex by P(II)-mediated sensing of 2-oxoglutarate. PLoS ONE. 2011;6:e26327 pubmed publisher
  49. Zoghbi M, Fuson K, Sutton R, Altenberg G. Kinetics of the association/dissociation cycle of an ATP-binding cassette nucleotide-binding domain. J Biol Chem. 2012;287:4157-64 pubmed publisher
    ..We proposed that based on their variable rates of hydrolysis, the rate-limiting step of the hydrolysis cycle may differ among full-length ABC proteins. ..
  50. Makarova K, Koonin E, Kelman Z. The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes. Biol Direct. 2012;7:7 pubmed publisher
    ..The inactivated RecJ homologs in several archaeal lineages most likely are dedicated structural components of replication complexes. ..
  51. Chemnitz Galal W, Pan M, Kelman Z, Hurwitz J. Characterization of DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis. J Biol Chem. 2012;287:16209-19 pubmed publisher
    ..Supplementation of such reactions with the DNA primase complex supported lagging strand formation as well...
  52. Naor A, Thiaville P, Altman Price N, Cohen Or I, Allers T, De Crecy Lagard V, et al. A genetic investigation of the KEOPS complex in halophilic Archaea. PLoS ONE. 2012;7:e43013 pubmed publisher
    ..volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t(6)A modification, and elevated levels of intra-cellular glycation products...
  53. Khomyakova M, B kmez z, Thomas L, Erb T, Berg I. A methylaspartate cycle in haloarchaea. Science. 2011;331:334-7 pubmed publisher
    ..Moreover, it requires elevated intracellular glutamate concentrations, as well as coupling carbon assimilation with nitrogen metabolism...