archaeal rna

Summary

Summary: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.

Top Publications

  1. Clouet d Orval B, Bortolin M, Gaspin C, Bachellerie J. 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. Nucleic Acids Res. 2001;29:4518-29 pubmed
  2. Tang T, Rozhdestvensky T, d Orval B, Bortolin M, Huber H, Charpentier B, et al. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res. 2002;30:921-30 pubmed
    ..This supports the notion that it might have an important but still unknown role in pre-rRNA biogenesis or might even target RNA molecules other than rRNA. ..
  3. Hainzl T, Huang S, Sauer Eriksson A. Structure of the SRP19 RNA complex and implications for signal recognition particle assembly. Nature. 2002;417:767-71 pubmed publisher
    ..The structure explains the role of SRP19 and provides a molecular framework for SRP54 binding and SRP assembly in Eukarya and Archaea...
  4. Ashelford K, Chuzhanova N, Fry J, Jones A, Weightman A. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol. 2006;72:5734-41 pubmed
    ..Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/. ..
  5. Srinivasan G, James C, Krzycki J. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science. 2002;296:1459-62 pubmed
    ..Charging a tRNA(CUA) with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Our results indicate that pyrrolysine is the 22nd genetically encoded natural amino acid...
  6. Fatica A, Tollervey D. Insights into the structure and function of a guide RNP. Nat Struct Biol. 2003;10:237-9 pubmed
  7. Kawarabayasi Y, Hino Y, Horikawa H, Jin no K, Takahashi M, Sekine M, et al. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 2001;8:123-40 pubmed
    ..The result suggests that this strain is closer to eukaryotes among the archaea strains so far sequenced. The data presented in this paper are also available on the internet homepage (http://www.bio.nite.go.jp/E-home/genome_list-e.html/)...
  8. Chen S, Lee W, Hottes A, Shapiro L, McAdams H. Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci U S A. 2004;101:3480-5 pubmed
    ..Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences. ..
  9. Moll R. The archaeal signal recognition particle: steps toward membrane binding. J Bioenerg Biomembr. 2004;36:47-53 pubmed
    ..Investigations of the archaeal SRP pathway could therefore identify novel aspects of this process not previously reported or unique to archaea when compared with the respective eukaryal and bacterial systems. ..

More Information

Publications62

  1. Starostina N, Marshburn S, Johnson L, Eddy S, Terns R, Terns M. Circular box C/D RNAs in Pyrococcus furiosus. Proc Natl Acad Sci U S A. 2004;101:14097-101 pubmed
    ..Moreover, the unexpected discovery of circular box C/D RNAs points to the existence of a previously unrecognized biogenesis pathway for box C/D RNAs in archaea...
  2. Zwieb C, van Nues R, Rosenblad M, Brown J, Samuelsson T. A nomenclature for all signal recognition particle RNAs. RNA. 2005;11:7-13 pubmed
    ..In order to assist in the continuation of these studies, we propose an SRP RNA nomenclature applicable to the three divisions of life. ..
  3. Renalier M, Joseph N, Gaspin C, Thebault P, Mougin A. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA. 2005;11:1051-63 pubmed publisher
    ..In this archaea, the C56 2'-O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs...
  4. Zhang X, Champion E, Tran E, Brown B, Baserga S, Maxwell E. The coiled-coil domain of the Nop56/58 core protein is dispensable for sRNP assembly but is critical for archaeal box C/D sRNP-guided nucleotide methylation. RNA. 2006;12:1092-103 pubmed
  5. Portnoy V, Schuster G. RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Res. 2006;34:5923-31 pubmed
    ..This ribonuclease is not able to degrade structured RNA better than PNPase. RNase R, which appears to be the only exoribonucleases in Haloferax volcanii, was found to be essential for viability. ..
  6. Yurist S, Dahan I, Eichler J. SRP19 is a dispensable component of the signal recognition particle in Archaea. J Bacteriol. 2007;189:276-9 pubmed publisher
    ..The absence of SRP19 did, however, increase membrane bacterioruberin levels...
  7. Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, et al. SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol. 2006;6:411-8 pubmed
    ..7%), and known split tRNAs (100%). Our program will be very useful for identifying novel tRNA genes after completion of genome projects. The SPLITS source code is freely downloadable at http://splits.iab.keio.ac.jp/...
  8. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K, et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol. 2008;31:241-50 pubmed publisher
  9. Cole J, Wang Q, Cardenas E, Fish J, Chai B, Farris R, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37:D141-5 pubmed publisher
    ..Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/. ..
  10. Galand P, Casamayor E, Kirchman D, Potvin M, Lovejoy C. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 2009;3:860-9 pubmed publisher
    ..Our results unveiled for the first time an archaeal community dominated by group III Euryarchaeota and show biogeographical traits for marine Arctic Archaea. ..
  11. Wang H, Hickey D. Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res. 2002;30:2501-7 pubmed
    ..This provides compelling evidence for strong stabilizing selection acting on 16S rRNA single-stranded regions. We found that selection favors purines (A+G), and especially adenine (A), in the single-stranded regions of these rRNAs. ..
  12. Rozhdestvensky T, Tang T, Tchirkova I, Brosius J, Bachellerie J, H ttenhofer A. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res. 2003;31:869-77 pubmed
    ..These findings suggest a triple role for L7Ae protein in Archaea, e.g. in ribosomes as well as H/ACA and C/D box sRNP biogenesis and function by binding to the K-turn motif...
  13. Speckmann W, Li Z, Lowe T, Eddy S, Terns R, Terns M. Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus. Curr Biol. 2002;12:199-203 pubmed
    ..Our studies have revealed the remarkable ability of archaeal Box C/D RNAs to assemble into functional RNA-protein complexes in the eukaryotic nucleus. ..
  14. Tang T, Bachellerie J, Rozhdestvensky T, Bortolin M, Huber H, Drungowski M, et al. Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci U S A. 2002;99:7536-41 pubmed
    ..Our study further supports the importance of snmRNAs in all three domains of life...
  15. Gurha P, Joardar A, Chaurasia P, Gupta R. Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation. RNA Biol. 2007;4:101-9 pubmed
    ..Conserved A58 in tRNA normally forms a tertiary reverse Hoogstein base pair with an equally conserved U54. This base pair is recognized by TruB. Apparently aCbf5 does not require this base pair to recognize U55 for conversion to Psi55. ..
  16. Lorentzen E, Conti E. Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol Cell. 2005;20:473-81 pubmed
    ..The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome. ..
  17. Nolivos S, Carpousis A, Clouet d Orval B. The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn. Nucleic Acids Res. 2005;33:6507-14 pubmed
    ..For the C/D guides with a 3 nt-spacer we show that the sequence and length is also important. The K-loop could improve the stability of the C/D guide RNAs in Pyrococcal species, which are extreme hyperthermophiles...
  18. Ramos C, Oliveira C, Torriani I, Oliveira C. The Pyrococcus exosome complex: structural and functional characterization. J Biol Chem. 2006;281:6751-9 pubmed
    ..The results shown here also indicate the participation of the exosome in RNA metabolism in Archaea, as was established in Eukarya...
  19. Hall T, Brown J. Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins. RNA. 2002;8:296-306 pubmed
    ..RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus...
  20. Huber H, Hohn M, Rachel R, Fuchs T, Wimmer V, Stetter K. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature. 2002;417:63-7 pubmed
    ..N. equitans' harbours the smallest archaeal genome; it is only 0.5 megabases in size. This organism will provide insight into the evolution of thermophily, of tiny genomes and of interspecies communication. ..
  21. Cannone J, Subramanian S, Schnare M, Collett J, D Souza L, Du Y, et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2 pubmed
    ..rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site. ..
  22. Zahler N, Christian E, Harris M. Recognition of the 5' leader of pre-tRNA substrates by the active site of ribonuclease P. RNA. 2003;9:734-45 pubmed
    ..These results provide the first direct evidence for RNase P RNA interactions with the substrate cleavage site, and show that RNA and protein cooperate in leader sequence recognition. ..
  23. Koonin E, Makarova K, Elkins J. Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota". Biol Direct. 2007;2:38 pubmed
    ..These findings suggest that all 12 core subunits of eukaryotic RNAPs were already present in the last common ancestor of the extant archaea...
  24. Randau L, Schröder I, Soll D. Life without RNase P. Nature. 2008;453:120-3 pubmed publisher
    ..These findings demonstrate how nature can cope with the loss of the universal and supposedly ancient RNase P through genomic rearrangement at tRNA genes under the pressure of genome condensation...
  25. Sugahara J, Kikuta K, Fujishima K, Yachie N, Tomita M, Kanai A. Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol. 2008;25:2709-16 pubmed publisher
    ..The sequences and secondary structures of the tRNA genes and their bulge-helix-bulge motifs were registered in SPLITSdb (http://splits.iab.keio.ac.jp/splitsdb/), a novel and comprehensive database for archaeal tRNA genes...
  26. Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R. The European database on small subunit ribosomal RNA. Nucleic Acids Res. 2002;30:183-5 pubmed
    ..Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available. ..
  27. Rosenblad M, Larsen N, Samuelsson T, Zwieb C. Kinship in the SRP RNA family. RNA Biol. 2009;6:508-16 pubmed
    ..Updates of the Rfam SRP RNA sequence collection are expected to benefit from the suggested groupings. ..
  28. Santangelo T, Reeve J. Deletion of switch 3 results in an archaeal RNA polymerase that is defective in transcript elongation. J Biol Chem. 2010;285:23908-15 pubmed publisher
    ..The close structural homology of archaeal and eukaryotic RNAPs would predict that eukaryotic Switch 3 loops likely conform to the archaeal rather than bacterial functional paradigm. ..
  29. Aittaleb M, Rashid R, Chen Q, Palmer J, Daniels C, Li H. Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol. 2003;10:256-63 pubmed publisher
    ..A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data...
  30. Schmeing T, Moore P, Steitz T. Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. RNA. 2003;9:1345-52 pubmed
    ..It appears that the E site on the 50S subunit was formed by only RNA in the last common ancestor of the three kingdoms, since the proteins at the E sites of H. marismortui and Deinucoccus radiodurans large subunits are not homologous. ..
  31. Kirpekar F, Hansen L, Rasmussen A, Poehlsgaard J, Vester B. The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA. J Mol Biol. 2005;348:563-73 pubmed
    ..Our results show that all the modified positions are at regions with RNA-RNA contacts and all except one are at the surface of the subunit and in functionally important regions...
  32. Nikulin A, Eliseikina I, Tishchenko S, Nevskaya N, Davydova N, Platonova O, et al. Structure of the L1 protuberance in the ribosome. Nat Struct Biol. 2003;10:104-8 pubmed publisher
    ..Incorporation of the L1-rRNA complex into the structural models of the T. thermophilus 70S ribosome and the Deinococcus radiodurans 50S subunit gives a reliable representation of most of the L1 protuberance within the ribosome...
  33. Razga F, Spacková N, Réblová K, Koca J, Leontis N, Sponer J. Ribosomal RNA kink-turn motif--a flexible molecular hinge. J Biomol Struct Dyn. 2004;22:183-94 pubmed
    ..They can for example be involved in mediation of large-scale motions or they can allow a smooth assembling of the other parts of the ribosome...
  34. Tocchini Valentini G, Fruscoloni P, Tocchini Valentini G. Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc Natl Acad Sci U S A. 2005;102:8933-8 pubmed
    ..The last-named enzyme, arising most likely by gene duplication and subsequent "subfunctionalization," requires the products of both genes to be active. ..
  35. Ziesche S, Omer A, Dennis P. RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea. Mol Microbiol. 2004;54:980-93 pubmed publisher
    ..Maximal activity of double guide sRNAs required that both methylation sites be present in cis on the target RNA...
  36. Spitalny P, Thomm M. Analysis of the open region and of DNA-protein contacts of archaeal RNA polymerase transcription complexes during transition from initiation to elongation. J Biol Chem. 2003;278:30497-505 pubmed
    ..This study shows characteristic mechanistic properties of the archaeal system and also similarities to prokaryotic RNAP and pol II. ..
  37. Xu Y, Amero C, Pulukkunat D, Gopalan V, Foster M. Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-R. J Mol Biol. 2009;393:1043-55 pubmed publisher
    ..These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme. ..
  38. Rother M, Resch A, Wilting R, Bock A. Selenoprotein synthesis in archaea. Biofactors. 2001;14:75-83 pubmed
    ..The use of the genetic system of M. maripaludis allowed the heterologous expression of a selenoprotein gene from M. jannaschii and will facilitate the elucidation of the mechanism of the selenocysteine insertion process in the future. ..
  39. Lorentzen E, Conti E. Expression, reconstitution, and structure of an archaeal RNA degrading exosome. Methods Enzymol. 2008;447:417-35 pubmed publisher
    ..Furthermore, we describe several crystal structures in which RNA substrates were diffused into crystals and how anomalous scattering from 5-iodo-uridine-modified RNA was used to locate low-occupancy RNA binding sites. ..
  40. Marck C, Grosjean H. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA. 2003;9:1516-31 pubmed
  41. Li Y, Altman S. In search of RNase P RNA from microbial genomes. RNA. 2004;10:1533-40 pubmed
    ..The catalytic center of this RNA, and its detection from some environmental whole genome shotgun sequences, is also discussed. ..
  42. Bachellerie J, Cavaille J, Huttenhofer A. The expanding snoRNA world. Biochimie. 2002;84:775-90 pubmed
    ..Recent characterization of homologs of eukaryotic modification guide snoRNAs in Archaea reveals the ancient origin of these non-coding RNA families and offers new perspectives as to their range of function. ..
  43. Terns M, Terns R. Small nucleolar RNAs: versatile trans-acting molecules of ancient evolutionary origin. Gene Expr. 2002;10:17-39 pubmed
    ..The unique properties of snoRNAs are now being harnessed for basic research and therapeutic applications. ..
  44. Parker J, Roe S, Barford D. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 2004;23:4727-37 pubmed
  45. Bini E, Dikshit V, Dirksen K, Drozda M, Blum P. Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus. RNA. 2002;8:1129-36 pubmed
    ..These are the first mRNA half-lives reported for a hyperthermophile or member of the crenarchaea. The unexpected stability of several transcripts has important implications for gene expression and mRNA degradation in this organism. ..
  46. Mallick B, Chakrabarti J, Sahoo S, Ghosh Z, Das S. Identity elements of archaeal tRNA. DNA Res. 2005;12:235-46 pubmed
    ..Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate tRNA-characteristics that delineate the different orders of Archaea. ..
  47. Zago M, Dennis P, Omer A. The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Microbiol. 2005;55:1812-28 pubmed
    ..solfataricus contains a plethora of small RNAs. Most of these are bound directly by the L7Ae protein; the others may well be part of larger, transiently stable RNP complexes that contain the L7Ae protein as core component. ..
  48. Nunoura T, Hirayama H, Takami H, Oida H, Nishi S, Shimamura S, et al. Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ Microbiol. 2005;7:1967-84 pubmed
    ..The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota. ..
  49. Randau L, Pearson M, Soll D. The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett. 2005;579:2945-7 pubmed
    ..Sci. USA 100, 12984-12988]. Along with a previously unidentified joined tRNA(Gln) (UUG), Nanoarchaeum equitans exhibits 44 tRNAs and is enabled to read all 61 sense codons. Features unique to this set of tRNA molecules are discussed...
  50. Hainzl T, Huang S, Sauer Eriksson A. Structural insights into SRP RNA: an induced fit mechanism for SRP assembly. RNA. 2005;11:1043-50 pubmed
    ..Binding of SRP19 to 7S RNA reveals an elegant mechanism of how protein-induced changes are directed through an RNA molecule and may relate to those regulating the assembly of other RNPs. ..
  51. Portnoy V, Evguenieva Hackenberg E, Klein F, Walter P, Lorentzen E, Klug G, et al. RNA polyadenylation in Archaea: not observed in Haloferax while the exosome polynucleotidylates RNA in Sulfolobus. EMBO Rep. 2005;6:1188-93 pubmed
    ..Together, our results identify the first organism without RNA polyadenylation and show a polyadenylation activity of the archaea exosome...
  52. Schmitt E, Panvert M, Blanquet S, Mechulam Y. Structural basis for tRNA-dependent amidotransferase function. Structure. 2005;13:1421-33 pubmed publisher
    ..Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE...
  53. Clouet d Orval B, Gaspin C, Mougin A. Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. Biochimie. 2005;87:889-95 pubmed
    ..In addition to their role in modification, both modification enzymes and C/D guide RNPs may have a chaperone function insuring the precise folding of the mature, functional tRNA. ..