RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

[1]  Tsutomu Suzuki,et al.  The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon , 2008, The EMBO journal.

[2]  Priyatansh Gurha,et al.  Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP. , 2008, RNA.

[3]  Shigeyuki Yokoyama,et al.  Structure, dynamics, and function of RNA modification enzymes. , 2008, Current opinion in structural biology.

[4]  A. Marchfelder,et al.  Maturation of the 5S rRNA 5' end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii. , 2008, RNA.

[5]  Zhili Xu,et al.  A conserved rRNA methyltransferase regulates ribosome biogenesis , 2008, Nature Structural &Molecular Biology.

[6]  J. Vandenhaute,et al.  The conserved Wobble uridine tRNA thiolase Ctu1–Ctu2 is required to maintain genome integrity , 2008, Proceedings of the National Academy of Sciences.

[7]  Paul F Agris,et al.  tRNA's modifications bring order to gene expression. , 2008, Current opinion in microbiology.

[8]  A. Blomberg,et al.  Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping. , 2008, RNA.

[9]  C. Chow,et al.  pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA. , 2008, RNA.

[10]  S. Thakur,et al.  Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli , 2008, The EMBO journal.

[11]  J. Cate,et al.  Structural Insights into ribosome recycling factor interactions with the 70S ribosome. , 2008, Journal of molecular biology.

[12]  I. Behm-Ansmant,et al.  Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs , 2008, Nucleic acids research.

[13]  John SantaLucia,et al.  Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA. , 2008, Journal of molecular biology.

[14]  B. Golinelli‐Pimpaneau,et al.  Acquisition of a bacterial RumA‐type tRNA(uracil‐54, C5)‐methyltransferase by Archaea through an ancient horizontal gene transfer , 2007, Molecular microbiology.

[15]  J. Chakrabarti,et al.  Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui. , 2007, RNA.

[16]  Maurille J. Fournier,et al.  The 3D rRNA modification maps database: with interactive tools for ribosome analysis , 2007, Nucleic Acids Res..

[17]  I-Min A. Chen,et al.  The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions , 2007, Nucleic Acids Res..

[18]  HaroldC. Smith.  RNA and DNA editing : molecular mechanisms and their integration into biological systems , 2008 .

[19]  P. Blum.  Archaea : new models for prokaryotic biology , 2008 .

[20]  M. Fournier,et al.  rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity. , 2007, Molecular cell.

[21]  M. Sørensen,et al.  Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination , 2007, Proceedings of the National Academy of Sciences.

[22]  M. Helm.  Post-transcriptional nucleotide modification and alternative folding of RNA , 2007, Nucleic Acids Research.

[23]  M. Inouye,et al.  Dissection of 16S rRNA Methyltransferase (KsgA) Function in Escherichia coli , 2007, Journal of bacteriology.

[24]  S. K. Mahto,et al.  Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications. , 2007, ACS chemical biology.

[25]  E. Maxwell,et al.  The Box C/D RNPS: Evolutionarily Ancient Nucleotide Modification Complexes , 2007 .

[26]  A. Byström,et al.  A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast. , 2007, RNA.

[27]  S. Douthwaite,et al.  Archease from Pyrococcus abyssi Improves Substrate Specificity and Solubility of a tRNA m5C Methyltransferase* , 2007, Journal of Biological Chemistry.

[28]  P. Herdewijn,et al.  Post-transcriptional modification mapping in the Clostridium acetobutylicum 16S rRNA by mass spectrometry and reverse transcriptase assays , 2007, Nucleic acids research.

[29]  Priyatansh Gurha,et al.  Differential Roles of Archaeal Box H/ACA Proteins in Guide RNA-Dependent and Independent Pseudouridine Formation , 2007, RNA biology.

[30]  Wayne A. Decatur,et al.  New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. , 2007, RNA.

[31]  R. Guymon,et al.  Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine. , 2007, RNA.

[32]  A. Joachimiak,et al.  Methyltransferase That Modifies Guanine 966 of the 16 S rRNA , 2007, Journal of Biological Chemistry.

[33]  J. Dinman,et al.  Optimization of Ribosome Structure and Function by rRNA Base Modification , 2007, PloS one.

[34]  Fangfang Xia,et al.  The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation , 2006, Nucleic Acids Res..

[35]  Ikuo Uchiyama,et al.  MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups , 2006, Nucleic Acids Res..

[36]  A. Oren.  Biodiversity in Highly Saline Environments , 2007 .

[37]  T. Oshima,et al.  How Nucleic Acids Cope with High Temperature , 2007 .

[38]  N. Glansdorff,et al.  Physiology and biochemistry of extremophiles. , 2007 .

[39]  D. Madern,et al.  Molecular Adaptation to High Salt , 2007 .

[40]  V. de Crécy-Lagard,et al.  Comparative RNomics and Modomics in Mollicutes: Prediction of Gene Function and Evolutionary Implications , 2007, IUBMB life.

[41]  V. de Crécy-Lagard.  Identification of genes encoding tRNA modification enzymes by comparative genomics. , 2007, Methods in enzymology.

[42]  C. Branlant,et al.  A dedicated computational approach for the identification of archaeal H/ACA sRNAs. , 2007, Methods in enzymology.

[43]  Harry F. Noller,et al.  Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements , 2014, Cell.

[44]  Janusz M. Bujnicki,et al.  Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases , 2007, BMC Bioinformatics.

[45]  T. Allers,et al.  Regulated Polyploidy in Halophilic Archaea , 2006, PloS one.

[46]  Bo Huang,et al.  Elevated levels of two tRNA species bypass the requirement for elongator complex in transcription and exocytosis. , 2006, Molecular cell.

[47]  M. Selmer,et al.  Structure of the 70S Ribosome Complexed with mRNA and tRNA , 2006, Science.

[48]  Simon de Givry,et al.  Searching RNA motifs and their intermolecular contacts with constraint networks , 2020 .

[49]  R. Terns,et al.  Formation of the conserved pseudouridine at position 55 in archaeal tRNA , 2006, Nucleic acids research.

[50]  H. Mori,et al.  Bmc Molecular Biology the Yfhq Gene of Escherichia Coli Encodes a Trna:cm32/um32 Methyltransferase , 2022 .

[51]  Tsutomu Suzuki,et al.  Conserved Loop Sequence of Helix 69 in Escherichia coli 23 S rRNA Is Involved in A-site tRNA Binding and Translational Fidelity* , 2006, Journal of Biological Chemistry.

[52]  S. Douthwaite,et al.  YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. , 2006, Journal of molecular biology.

[53]  J. L. Jennings,et al.  Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. , 2006, Genes & development.

[54]  Pooja M. Desai,et al.  Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution. , 2006, RNA.

[55]  B. Dujon,et al.  The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications , 2006, Nucleic acids research.

[56]  Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus. , 2006, Biochemistry.

[57]  K. Rudd,et al.  Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. , 2006, RNA.

[58]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[59]  Mark Helm,et al.  Post-transcriptional nucleotide modification and alternative folding of RNA , 2006, Nucleic acids research.

[60]  Tsutomu Suzuki,et al.  Temperature-dependent Biosynthesis of 2-Thioribothymidine of Thermus thermophilus tRNA* , 2006, Journal of Biological Chemistry.

[61]  A. Hopper,et al.  Modified view of tRNA: stability amid sequence diversity. , 2006, Molecular cell.

[62]  Feng Chen,et al.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..

[63]  Katherine S. Pollard,et al.  The UCSC Archaeal Genome Browser , 2005, Nucleic Acids Res..

[64]  A. Ferré-D’Amaré,et al.  Pseudouridine synthases. , 2006, Chemistry & biology.

[65]  A. Omer,et al.  Small non-coding RNAs in Archaea. , 2005, Current opinion in microbiology.

[66]  I. Tanaka,et al.  Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S‐adenosyl‐L‐homocysteine , 2005, Proteins: Structure, Function, and Bioinformatics.

[67]  G. Björk,et al.  DOMAIN 4 SYNTHESIS AND PROCESSING OF MACROMOLECULES Transfer RNA Modification , 2013 .

[68]  G. Klebe,et al.  Mechanism and Substrate Specificity of tRNA–Guanine Transglycosylases (TGTs): tRNA‐Modifying Enzymes from the Three Different Kingdoms of Life Share a Common Catalytic Mechanism , 2005, Chembiochem : a European journal of chemical biology.

[69]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[70]  C. Gaspin,et al.  Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. , 2005, Biochimie.

[71]  Lawrence J. Clos,et al.  Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA. , 2005, RNA.

[72]  S. Clarke,et al.  A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA. , 2005, Biochemical and biophysical research communications.

[73]  JamesC . Anderson,et al.  The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. , 2005, RNA.

[74]  Ü. Maiväli,et al.  Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis , 2005, BMC Molecular Biology.

[75]  A. Hopper.  Faculty Opinions recommendation of The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. , 2005 .

[76]  P. Thébault,et al.  The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. , 2005, RNA.

[77]  Katherine H. Huang,et al.  The MicrobesOnline Web site for comparative genomics. , 2005, Genome research.

[78]  Daniel L Baker,et al.  RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. , 2005, Genes & development.

[79]  L. H. Hansen,et al.  The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA. , 2005, Journal of molecular biology.

[80]  Bo Huang,et al.  An early step in wobble uridine tRNA modification requires the Elongator complex. , 2005, RNA.

[81]  A. Omer,et al.  The expanding world of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus , 2005, Molecular microbiology.

[82]  J. Ofengand,et al.  Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans. , 2005, RNA.

[83]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[84]  Jef Rozenski,et al.  The Small Subunit rRNA Modification Database , 2004, Nucleic Acids Res..

[85]  M. Ginzburg,et al.  Ion metabolism in aHalobacterium , 1971, The Journal of Membrane Biology.

[86]  Henri Grosjean,et al.  Fine-tuning of RNA functions by modification and editing , 2005 .

[87]  S. K. Purushothaman,et al.  Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. , 2004, Molecular cell.

[88]  Elizabeth J. Tran,et al.  Sequential 2′-O-Methylation of Archaeal Pre-tRNATrp Nucleotides Is Guided by the Intron-encoded but trans-Acting Box C/D Ribonucleoprotein of Pre-tRNA* , 2004, Journal of Biological Chemistry.

[89]  S. Douthwaite,et al.  Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase. , 2004, RNA.

[90]  S. J. Nasvall,et al.  The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. , 2004, RNA.

[91]  J. Bujnicki,et al.  N2-Methylation of Guanosine at Position 10 in tRNA Is Catalyzed by a THUMP Domain-containing, S-Adenosylmethionine-dependent Methyltransferase, Conserved in Archaea and Eukaryota*[boxs] , 2004, Journal of Biological Chemistry.

[92]  C. Evilia,et al.  Distinct origins of tRNA(m1G37) methyltransferase. , 2004, Journal of molecular biology.

[93]  Marcin Feder,et al.  Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases. , 2004, Nucleic acids research.

[94]  G. Björk,et al.  Enzymatic conversion of cytidine to lysidine in anticodon of bacterial tRNAIle – an alternative way of RNA editing , 2004 .

[95]  A. Byström,et al.  The Saccharomyces cerevisiae TAN1 gene is required for N4-acetylcytidine formation in tRNA. , 2004, RNA.

[96]  J. Remme,et al.  Definition of bases in 23S rRNA essential for ribosomal subunit association. , 2004, RNA.

[97]  G. Björk,et al.  Formation of Thiolated Nucleosides Present in tRNA from Salmonella enterica serovar Typhimurium Occurs in Two Principally Distinct Pathways , 2004, Journal of bacteriology.

[98]  P. Agris.  Decoding the genome: a modified view. , 2004, Nucleic acids research.

[99]  J. Bujnicki,et al.  A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. , 2004, Nucleic acids research.

[100]  H. Larsen,et al.  Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement , 1975, Archives of Microbiology.

[101]  S. Clarke,et al.  Novel Methyltransferase for Modified Uridine Residues at the Wobble Position of tRNA , 2003, Molecular and Cellular Biology.

[102]  Henri Grosjean,et al.  Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. , 2003, RNA.

[103]  Shigeyuki Yokoyama,et al.  SURVEY AND SUMMARY: Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons , 2003, Nucleic acids research.

[104]  J. Bachellerie,et al.  In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp). , 2003, Nucleic acids research.

[105]  G. Lutfalla,et al.  Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast. , 2003, Molecular cell.

[106]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[107]  Naotake Ogasawara,et al.  An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. , 2003, Molecular cell.

[108]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[109]  J. Ofengand,et al.  A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. , 2003, RNA.

[110]  J. Bujnicki,et al.  Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. , 2003, Nucleic acids research.

[111]  M. Fournier,et al.  Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. , 2003, Molecular cell.

[112]  A. Hüttenhofer,et al.  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. , 2003, Nucleic acids research.

[113]  A. Hopper,et al.  tRNA transfers to the limelight. , 2003, Genes & development.

[114]  V. Ramakrishnan,et al.  Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form , 2002, Cell.

[115]  T. Henkin.  Faculty Opinions recommendation of tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. , 2002 .

[116]  Henri Grosjean,et al.  tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. , 2002, RNA.

[117]  A. Hüttenhofer,et al.  The expanding snoRNA world. , 2002, Biochimie.

[118]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[119]  W. Keller,et al.  tadA, an essential tRNA‐specific adenosine deaminase from Escherichia coli , 2002, The EMBO journal.

[120]  Wayne A. Decatur,et al.  rRNA modifications and ribosome function. , 2002, Trends in biochemical sciences.

[121]  A. Omer,et al.  In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[122]  J. Bujnicki,et al.  MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase , 2002, The EMBO journal.

[123]  M. Hansen,et al.  Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. , 2002, RNA.

[124]  C Gaspin,et al.  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. , 2001, Nucleic acids research.

[125]  V. Ramakrishnan,et al.  Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit , 2001, Science.

[126]  T. Lowe,et al.  A guided tour: small RNA function in Archaea , 2001, Molecular microbiology.

[127]  E. Koonin,et al.  TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. , 2001, FEMS microbiology letters.

[128]  T. Earnest,et al.  Crystal Structure of the Ribosome at 5.5 Å Resolution , 2001, Science.

[129]  Jorge F. Reyes-Spindola,et al.  Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. , 2001, Nucleic acids research.

[130]  V. Ramakrishnan,et al.  Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics , 2000, Nature.

[131]  D. T. Fox,et al.  Hypermodification of tRNA in Thermophilic Archaea , 2000, The Journal of Biological Chemistry.

[132]  J. Kowalak,et al.  Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii * , 2000, The Journal of Biological Chemistry.

[133]  T. Steitz,et al.  The structural basis of ribosome activity in peptide bond synthesis. , 2000, Science.

[134]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[135]  E. Binet,et al.  The FtsJ/RrmJ Heat Shock Protein of Escherichia coli Is a 23 S Ribosomal RNA Methyltransferase* , 2000, The Journal of Biological Chemistry.

[136]  J. Bachellerie,et al.  Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. , 2000, Journal of molecular biology.

[137]  S. Douthwaite,et al.  Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. , 2000, RNA.

[138]  D. T. Fox,et al.  CLONING, OVEREXPRESSION, AND CHARACTERIZATION OF tRNA-GUANINE TRANSGLYCOSYLASE FROM METHANOCOCCUS JANNASCHII* , 2000 .

[139]  W. Keller,et al.  An adenosine deaminase that generates inosine at the wobble position of tRNAs. , 1999, Science.

[140]  R. Green,et al.  Base-pairing between 23S rRNA and tRNA in the ribosomal A site. , 1999, Molecular cell.

[141]  Y. Motorin,et al.  Characterisation and enzymatic properties of tRNA(guanine 26, N (2), N (2))-dimethyltransferase (Trm1p) from Pyrococcus furiosus. , 1999, Journal of molecular biology.

[142]  Y. Motorin,et al.  Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. , 1999, RNA.

[143]  C. Abad-Zapatero,et al.  The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. , 1999, Journal of molecular biology.

[144]  D. Santi,et al.  Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli. , 1999, Biochemistry.

[145]  Y. Motorin,et al.  Transfer RNA modification enzymes from Pyrococcus furiosus: detection of the enzymatic activities in vitro. , 1999, Nucleic acids research.

[146]  L. Aravind,et al.  Novel Predicted RNA-Binding Domains Associated with the Translation Machinery , 1999, Journal of Molecular Evolution.

[147]  H. Michel,et al.  Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli. , 1999, Biochemistry.

[148]  J Ofengand,et al.  Purification, Cloning, and Characterization of the 16 S RNA m2G1207 Methyltransferase from Escherichia coli * , 1999, The Journal of Biological Chemistry.

[149]  Jef Rozenski,et al.  The RNA Modification Database: 1999 update , 1999, Nucleic Acids Res..

[150]  R Giegé,et al.  Universal rules and idiosyncratic features in tRNA identity. , 1998, Nucleic acids research.

[151]  W. Keller,et al.  Tad1p, a yeast tRNA‐specific adenosine deaminase, is related to the mammalian pre‐mRNA editing enzymes ADAR1 and ADAR2 , 1998, The EMBO journal.

[152]  D. Tollervey,et al.  Yeast 18S rRNA Dimethylase Dim1p: a Quality Control Mechanism in Ribosome Synthesis? , 1998, Molecular and Cellular Biology.

[153]  E. Hurt,et al.  Characterization of Yeast Protein Deg1 as Pseudouridine Synthase (Pus3) Catalyzing the Formation of Ψ38 and Ψ39 in tRNA Anticodon Loop* , 1998, The Journal of Biological Chemistry.

[154]  M. Winkler.  Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes , 1998 .

[155]  G. Björk,et al.  Links between tRNA Modification and Metabolism and Modified Nucleosides as Tumor Markers , 1998 .

[156]  Henri Grosjean,et al.  Modification And Editing Of Rna , 1998 .

[157]  James A. McCloskey,et al.  The RNA modification database--1998 , 1998, Nucleic Acids Res..

[158]  A novel dCMP methylase by engineering thymidylate synthase. , 1997, Biochemistry.

[159]  R. Planta,et al.  The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs. , 1997, Nucleic acids research.

[160]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[161]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[162]  Mark Proctor,et al.  The Solution Structure of the S1 RNA Binding Domain: A Member of an Ancient Nucleic Acid–Binding Fold , 1997, Cell.

[163]  S. Auxilien,et al.  Mechanism, specificity and general properties of the yeast enzyme catalysing the formation of inosine 34 in the anticodon of transfer RNA. , 1996, Journal of molecular biology.

[164]  J. Ballesta,et al.  A sparsomycin-resistant mutant of Halobacterium salinarium lacks a modification at nucleotide U2603 in the peptidyl transferase centre of 23 S rRNA. , 1996, Journal of molecular biology.

[165]  P. Agris,et al.  The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. , 1996, Progress in nucleic acid research and molecular biology.

[166]  James A. McCloskey,et al.  The Rna Modification Database , 1999 .

[167]  J. Ofengand,et al.  Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. , 1995, RNA.

[168]  H F Noller,et al.  Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site , 1995, Science.

[169]  H. Grosjean,et al.  A novel enzymatic pathway leading to 1-methylinosine modification in Haloferax volcanii tRNA. , 1995, Nucleic acids research.

[170]  J. Kowalak,et al.  The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. , 1994, Biochemistry.

[171]  P. Limbach,et al.  Summary: the modified nucleosides of RNA. , 1994, Nucleic acids research.

[172]  T. Oshima,et al.  Effects of unusual polyamines on phenylalanyl-tRNA formation. , 1994, Journal of biochemistry.

[173]  E. Koonin,et al.  SpoU protein of Escherichia coli belongs to a new family of putative rRNA methylases. , 1993, Nucleic acids research.

[174]  T. Oshima,et al.  Effects of novel polyamines on cell-free polypeptide synthesis catalyzed by Thermus thermophilus HB8 extract. , 1993, Journal of biochemistry.

[175]  B. C. Persson.  Modification of tRNA as a regulatory device , 1993, Molecular microbiology.

[176]  J. Kowalak,et al.  5S rRNA modification in the hyperthermophilic archaea Sulfolobus solfataricus and Pyrodictium occultum , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[177]  P. Mitchell,et al.  Clustering of modified nucleotides at the functional center of bacterial ribosomal RNA , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[178]  M. Sekine,et al.  Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group. , 1992, Biochemistry.

[179]  H. Noller,et al.  Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. , 1990, Journal of molecular biology.

[180]  J. McCloskey,et al.  Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. , 1990, Methods in enzymology.

[181]  S. Yokoyama,et al.  Conformational characteristics of 4-acetylcytidine found in tRNA. , 1989, Nucleic acids symposium series.

[182]  A. Matsuda,et al.  A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli , 1989, The Journal of biological chemistry.

[183]  Yoshiyuki Kuchino,et al.  Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification , 1988, Nature.

[184]  R. Garrett,et al.  The importance of highly conserved nucleotides in the binding region of chloramphenicol at the peptidyl transfer centre of Escherichia coli 23S ribosomal RNA. , 1988, The EMBO journal.

[185]  Ramesh C. Gupta.  Transfer RNAs of Halobacterium volcanii: Sequences of five leucine and three serine tRNAs* , 1986 .

[186]  C. C. Marvel,et al.  Structural features of the hisT operon of Escherichia coli K-12. , 1985, Nucleic acids research.

[187]  R. Gupta.  Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. , 1984, The Journal of biological chemistry.

[188]  H. Noller,et al.  Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[189]  C. Woese,et al.  Sequence of the 16S Ribosomal RNA from Halobacterium volcanii, an Archaebacterium , 1983, Science.

[190]  L. H. Schulman,et al.  The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. , 1978, The Journal of biological chemistry.

[191]  M. Ginzburg,et al.  Ion Metabolism in a Halobacterium : I. Influence of age of culture on intracellular concentrations , 1970 .

[192]  S. Bayley,et al.  Codon assignments and fidelity of translation in a cell-free protein-synthesizing system from an extremely halophilic bacterium. , 1968, Canadian journal of biochemistry.